Gene site saturation mutagenesis

ABSTRACT

A method for producing progeny polynucleotides and polypeptides by Gene Site Saturation Mutagenesis (GSSM). The method provides a set of degenerate primers corresponding to codons of a template polynucleotide, and performs polymerase elongation to produce progeny polynucleotides, which contain sequences corresponding to the degenerate primers. The progeny polynucleotides can be expressed and screened for directed evolution.

This application is a continuation of U.S. Ser. No. 09/498,557, filedFeb. 4, 2000, now U.S. Pat. No. 6,713,279; which is acontinuation-in-part application of U.S. Ser. No. 09/495,052, filed Jan.31, 2000, now U.S. Pat. No. 6,479,258; which is a continuation-in-partapplication of U.S. Ser. No. 09/276,860, filed Mar. 26, 1999, now U.S.Pat. No. 6,352,842; which is a continuation-in-part application of U.S.Ser. No. 09/267,118, filed Mar. 9, 1999, now U.S. Pat. No. 6,238,884;which is a continuation-in-part application of U.S. Ser. No. 09/246,178,filed Feb. 4, 1999, now U.S. Pat. No. 6,171,820.

This application is also a continuation-in-part application of U.S. Ser.No. 10/223,507, filed Aug. 19, 2002, which is a continuation applicationof U.S. Ser. No. 09/495,052, filed Jan. 31, 2000, now U.S. Pat. No.6,479,258.

CONTENTS 1. GENERAL

-   -   1.1. FIELD OF THE INVENTION    -   1.2. BACKGROUND    -   13. SUMMARY OF THE INVENTION    -   1.4. BRIEF DESCRIPTION OF THE DRAWINGS

2. DETAILED DESCRIPTION OF THE INVENTION

-   -   2.1. DEFINITIONS    -   2.2. GENERAL CONSIDERATIONS & FORMATS FOR RECOMBINATION    -   2.3. VECTORS USED IN GENETIC VACCINATION        -   2.3.1. VIRAL VECTORS            -   2.3.1.1. ADENOVIRUSES            -   2.3.1.2. ADENO-ASSOCIATED VIRUS (AAV)            -   2.3.1.3. PAPILLOMA VIRUS            -   2.3.1.4. RETROVIRUSES        -   2.3.2. NON-VIRAL GENETIC VACCINE VECTORS    -   2.4. MULTICOMPONENT GENETIC VACCINES        -   2.4.1. VECTOR “AR”, DESIGNED TO PROVIDE OPTIMAL ANTIGEN            RELEASE        -   2.4.2. VECTOR COMPONENTS “CTL-DC”, “CTL-LC” AND “CTL-MM”I            DESIGNED FOR OPTIMAL PRODUCTION OF CTLs        -   2.4.3. VECTORS “M” DESIGNED FOR OPTIMAL RELEASE OF IMMUNE            MODULATORS        -   2.4.4. VECTORS “CK”, DESIGNED TO DIRECT RELEASE OF            CHEMOKINES        -   2.4.5. OTHER VECTORS    -   2.5. SCREENING METHODS        -   2.5.1. SCREENING FOR VECTOR LONGEVITY OR TRANSLOCATION TO            DESIRED TISSUE            -   2.5.1.1. SELECTION FOR EXPRESSION OF CELL                SURFACE-LOCALIZED ANTIGEN            -   2.5.1.2. SELECTION FOR EXPRESSION OF SECRETED                ANTIGEN/CYTOKINE/CHEMOKINE        -   2.5.2. FLOW CYTOMETRY        -   2.5.3. ADDITIONAL IN VITRO SCREENING METHODS        -   2.5.4. ANTIGEN LIBRARY IMMUNIZATION        -   2.5.5. SCREENING FOR OPTIMAL INDUCTION OF PROTECTIVE            IMMUNITY        -   2.5.6. SCREENING OF GENETIC VACCINE VECTORS THAT ACTIVATE            HUMAN ANTIGEN-SPECIFIC LYMPHOCYTE RESPONSES        -   2.5.7. SCID-HUMAN SKIN MODEL FOR VACCINATION STUDIES        -   2.5.8. MOUSE MODEL FOR STUDYING THE EFFICIENCY OF GENETIC            VACCINES IN TRANSFECTING HUMAN MUSCLE CELLS AND INDUCING            HUMAN IMMUNE RESPONSES IN VIVO        -   2.5.9. SCREENING FOR IMPROVED DELIVERY OF VACCINES        -   2.5.10. ENHANCED ENTRY OF GENETIC VACCINE VECTORS INTO CELLS    -   2.6. OPTIMIZATION OF GENETIC VACCINE COMPONENTS        -   2.6.1. EPISOMAL VECTOR MAINTENANCE        -   2.6.2. EVOLUTION OF OPTIMIZED PROMOTERS FOR EXPRESSION OF AN            ANTIGEN            -   2.6.2.1. CONSTITUTIVE PROMOTERS            -   2.6.2.2. CELL-SPECIFIC PROMOTERS            -   2.6.2.3. INDUCIBLE PROMOTERS        -   2.6.3. EVOLUTION OF BINDING POLYPEPTIDES THAT ENHANCE            SPECIFICITY AND EFFICIENCY OF GENETIC VACCINES        -   2.6.4. EVOLUTION OF BACTERIOPHAGE VECTORS            -   2.6.4.1. EVOLUTION OF EFFICIENT DELIVERY OF                BACTERIOPHAGE VEHICLES BY INHALATION OR ORAL DELIVERY            -   2.6.4.2. EVOLUTION OF BACTERIOPHAGE VEHICLES FOR                EFFICIENT HOMING TO APCs            -   2.6.4.3. EVOLUTION OF BACTERIOPHAGE FOR INVASION OF APCs        -   2.6.5. EVOLUTION OF IMPROVED IMMUNOMODULATORY SEQUENCES            -   2.6.5.1. IMMUNOSTIMULATORY DNA SEQUENCES            -   2.6.5.2. CYTOKINES, CHEMOKINES, AND ACCESSORY MOLECULES            -   2.6.5.3. AGONISTS OR ANTAGONISTS OF CELLULAR RECEPTORS            -   2.6.5.4. COSTIMULATORY MOLECULES CAPABLE OF INHIBITING                OR ENHANCING ACTIVATION, DIFFERENTIATION, OR ANERGY OF                ANTIGEN-SPECIFIC T CELLS        -   2.6.6. EVOLUTION OF GENETIC VACCINE VECTORS FOR INCREASED            VACCINATION EFFICACY AND EASE OF VACCINATION            -   2.6.6.1. TOPICAL APPLICATION OF GENETIC VACCINE VECTORS            -   2.6.6.2. ENHANCED ABILITY TO ESCAPE HOST IMMUNE SYSTEM            -   2.6.6.3. ENHANCED ANTIVIRAL ACTIVITY            -   2.6.6.4. EVOLUTION OF VECTORS HAVING INCREASED COPY                NUMBER IN PRODUCTION CELLS    -   2.7. OPTIMIZATION OF TRANSPORT AND PRESENTATION OF ANTIGENS        -   2.7.1. PROTEASOMES        -   2.7.2. ANTIGEN TRANSPORT        -   2.7.3. CYTOTOXIC T-CELL INDUCING SEQUENCES AND IMMUNOGENIC            AGONIST SEQUENCES    -   2.8. GENETIC VACCINE PHARMACEUTICAL COMPOSITIONS AND METHODS OF        ADMINISTRATION    -   2.9. USES OF GENETIC VACCINES        -   2.9.1. INFECTIOUS DISEASES            -   2.9.1.1. BACTERIAL PATHOGENS AND TOXINS            -   2.9.1.2. VIRAL PATHOGENS        -   2.9.2. INFLAMMATORY AND AUTOIMMUNE DISEASES        -   2.9.3. ALLERGY AND ASTHMA        -   2.9.4. CANCER        -   2.9.5. PARASITES        -   2.9.6. CONTRACEPTION    -   2.10. MALARIAL ANTIGENS AND VACCINES        -   2.10.1. MALARIAL POLYPEPTIDES        -   2.10.2. MALARIAL NUCLEIC ACIDS AND CELLS CAPABLE OF            EXPRESSING SAME        -   2.10.3. ANTIBODIES        -   2.10.4. METHODS OF USE            -   2.10.4.1. DIAGNOSTIC APPLICATIONS            -   2.10.4.2. SCREENING APPLICATIONS            -   2.10.4.3. THERAPEUTIC AND PROPHYLACTIC APPLICATIONS    -   2.11. DIRECTED EVOLUTION METHODS        -   2.11.1. SATURATION MUTAGENESIS        -   2.11.2. CHIMERIZATIONS            -   2.11.2.1. “SHUFFLING”            -   2.11.2.2. EXONUCLEASE-MEDIATED REASSEMBLY            -   2.11.2.3. NON-STOCHASTIC LIGATION REASSEMBLY            -   2.11.2.4. END-SELECTION        -   2.11.3. ADDITIONAL SCREENING METHODS

3. LITERATURE CITED 1. GENERAL 1.1. Field of the Invention

This invention pertains to the field of genetic vaccines. Specifically,the invention provides multi-component genetic vaccines that containcomponents that are optimized for a particular vaccination goal. In aparticular aspect this invention provides methods for improving theefficacy of genetic vaccines by providing materials that facilitatetargeting of a genetic vaccine to a particular tissue or cell type ofinterest.

This invention also pertains to the field of modulation of immuneresponses such as those induced by genetic vaccines and also pertains tothe field of methods for developing immunogens that can induce efficientimmune responses against a broad range of antigens.

Thus, the present invention also relates generally to novel proteins,and fragments thereof, as well as nucleic acids which encode theseproteins, and methods of making and using these proteins in diagnostic,prophylactic and therapeutic applications. In a particularexemplification, the present invention relates to proteins from thePlasmodium falciparum erythrocyte membrane protein 1 (“PfEMP1”) genefamily and fragments thereof which are derived from malaria parasitizederythrocytes. In particular, these proteins are derived from theerythrocyte membrane protein of Plasmodium falciparum parasitizederythrocytes, also termed “PfEMP1”. The present invention also providesnucleic acids encoding these proteins, which proteins and nucleic acidsare associated with the pathology of malaria infections, and which maybe used as vaccines or other prophylactic treatments for the preventionof malaria infections, and/or in diagnosing and treating the symptoms ofpatients who suffer from malaria and associated diseases.

This invention also relates to the field of protein engineering.Specifically, this invention relates to a directed evolution method forpreparing a polynucleotide encoding a polypeptide. More specifically,this invention relates to a method of using mutagenesis to generate anovel polynucleotide encoding a novel polypeptide, which novelpolypeptide is itself an improved biological molecule &/or contributesto the generation of another improved biological molecule. Morespecifically still, this invention relates to a method of performingboth non-stochastic polynucleotide chimerization and non-stochasticsite-directed point mutagenesis.

Thus, in one aspect, this invention relates to a method of generating aprogeny set of chimeric polynucleotide(s) by means that are syntheticand non-stochastic, and where the design of the progenypolynucleotide(s) is derived by analysis of a parental set ofpolynucleotides &/or of the polypeptides correspondingly encoded by theparental polynucleotides. In another aspect this invention relates to amethod of performing site-directed mutagenesis using means that areexhaustive, systematic, and non-stochastic.

Furthermore this invention relates to a step of selecting from among agenerated set of progeny molecules a subset comprised of particularlydesirable species, including by a process termed end-selection, whichsubset may then be screened further. This invention also relates to thestep of screening a set of polynucleotides for the production of apolypeptide &/or of another expressed biological molecule having auseful property.

Novel biological molecules whose manufacture is taught by this inventioninclude genes, gene pathways, and any molecules whose expression isaffected thereby, including directly encoded polypeptides &/or anymolecules affected by such polypeptides. Said novel biological moleculesinclude those that contain a carbohydrate, a lipid, a nucleic acid, &/ora protein component, and specific but non-limiting examples of theseinclude antibiotics, antibodies, enzymes, and steroidal andnon-steroidal hormones.

In a particular non-limiting aspect, the present invention relates toenzymes, particularly to thermostable enzymes, and to their generationby directed evolution. More particularly, the present invention relatesto thermostable enzymes which are stable at high temperatures and whichhave improved activity at lower temperatures.

1.2. Background

Providing Protective Immunity Even In Situations when the Pathogens arePoorly Characterized or Cannot be Isolated or Cultured in LaboratoryEnvironment.

Genetic immunization represents a novel mechanism of inducing protectivehumoral and cellular immunity. Vectors for genetic vaccinationsgenerally consist of DNA that includes a promoter/enhancer sequence, thegene of interest and a polyadenylation/transcriptional terminatorsequence. After intramuscular or intradermal injection, the gene ofinterest is expressed, followed by recognition of the resulting proteinby the cells of the immune system. Genetic immunizations provide meansto induce protective immunity even in situations when the pathogens arepoorly characterized or cannot be isolated or cultured in laboratoryenvironment.

Small Improvement in the Efficiency of Genetic Vaccine Vectors canResult in Dramatic Increase if the Level of Immune Response

The efficacy of genetic vaccination is often limited by inefficientuptake of genetic vaccine vectors into cells. Generally, less than 1% ofthe muscle or skin cells at the sites of injections express the gene ofinterest. Even a small improvement in the efficiency of genetic vaccinevectors to enter the cells can result in a dramatic increase in thelevel of immune response induced by genetic vaccination. A vectortypically has to cross many barriers which can result in only a veryminor fraction of the DNA ever being expressed.

Various Limitations to Immunogenicity

Limitations to immunogenicity include: loss of vector due to nucleasespresent in blood and tissues; inefficient entry of DNA into a cell;inefficient entry of DNA into the nucleus of the cell and preference ofDNA for other compartments; lack of DNA stability in the nucleus (factorlimiting nuclear stability may differ from those affecting othercellular and extracellular compartments), and, for vectors thatintegrate into the chromosome, the efficiency of integration and thesite of integration. Moreover, for many applications of geneticvaccines, it is preferable for the genetic vaccine to enter a particulartarget tissue or cell.

Thus, a need exists for genetic vaccines that can be targeted tospecific cell and tissue types of interest, and which exhibit anincreased ability to enter the target cells. The present inventionfulfills these and other needs.

Pathways for Immune Responses Induced by Genetic Vaccines

Elicitation of a desired in vivo response by a genetic vaccine generallyrequires multiple cellular processes in a complex sequence. Severalpotential pathways exist along which a genetic vaccine can exert itseffect on the mammalian immune system. In one pathway, the geneticvaccine vector enters cells that are the predominant cell type in thetissue that receives vaccine (e.g., muscle or epithelial cells). Thesecells express and release the antigen encoded by the vector. The vaccinevector can be engineered to have the antigen released as an intactprotein from living transfected cells (i.e., via a secretion process) ordirected to a membrane-bound form on the surface of these cells. Antigencan also be released from an intracellular compartment of such cells ifthose cells die.

The Antigen Derived from Vaccine Vector Internalization and AntigenExpression Within the Predominant Cell Type in the Tissue Ends Up withinAPC, which then Process the Antigen Internally to Prime MHC Class I andor Class II, Essential Steps in Activation of CD4⁺ T-Helper Cells andDevelopment of Potent Specific Immune Responses

Extracellular antigen derived from any of these situations interactswith antigen presenting cells (APC) either by binding to the cellsurface (specifically via IgM or via other non-immunoglobulin receptors)and subsequent endocytosis of outer membrane, or by fluid phasemicropinocytosis wherein the APC internalizes extracellular fluid andits contents into an endocytic compartment. Interaction with APC mayoccur before or after partial proteolytic cleavage in the extracellularenvironment. In any case, the antigen derived from vaccine vectorinternalization and antigen expression within the predominant cell typein the tissue ends up within APC. The APC then process the antigeninternally to prime MHC Class I and or Class II, essential steps inactivation of CD4⁺ T-helper cells (T_(H)1 and/or T_(H)2) and developmentof potent specific immune responses.

The Genetic Vaccine Plasmid Enters APC and Antigen is ProteolyticallyCleaved in the Cell Cytoplasm.

In a parallel pathway, the genetic vaccine plasmid enters APC (or thepredominant cell type in the tissue) and, instead of antigen derivedfrom plasmid expression being directed to extracellular export, antigenis proteolytically cleaved in the cell cytoplasm (in a proteasomedependent or independent process). Often, intracellular processing insuch cells occurs via proteasomal degradation into peptides that arerecognized by the TAP-1 and TAP-2 proteins and transported into thelumen of the rough endoplasmic reticulum (RER).

The Peptide Fragments are Transported into the RER Complex, Expressed onthe Cell Surface; in the Presence of Appropriate Additional Signals, canDifferentiate Into Functional CTLs.

The peptide fragments transported into the RER complex with MHC Class I.Such antigen fragments are then expressed on the cell surface inassociation with Class I. CD8⁺ cytotoxic T lymphocytes (CTL) bearingspecific T cell receptor then recognize the complex and can, in thepresence of appropriate additional signals, differentiate intofunctional CTLs.

By Virtue of Poorly Characterized Pathways for Trafficking ofCytoplasmically Generated Peptides into Endosomal Compartments, aGenetic Vaccine Vector can Lead to CD4⁺ T Cell Stimulation.

In addition, poorly characterized pathways, which are generally notdominant, exist in APC for trafficking of cytoplasmically generatedpeptides into endosomal compartments where they can end up complexedwith MHC Class II, and thereby act to present antigen peptides to CD4⁺T_(H)1 and T_(H)2 cells. Because activation, proliferation,differentiation and immunoglobulin isotype switching by B lymphocytesrequires help of CD4⁺ T cells, antigen presentation in the context ofMHC Class II molecules is crucial for induction of antigen-specificantibodies. By virtue of this pathway, a genetic vaccine vector can leadto CD4⁺ T cell stimulation in addition to the dominant CD8⁺ CTLactivation process described above. This alternative pathway is,however, of little consequence in muscle cells where levels of MHC ClassII expression are very low or zero.

In this Case Cytokines are Derived not Only from Processes Intrinsic tothe Interaction of DNA with Cells, or Specific Cell Responses to theAntigen, but Via Synthesis Directed by the Vaccine Plasmid.

Genetic vaccination can also elicit cytokine release from cells thatbind to or take up DNA. So-called immunostimulatory or adjuvantproperties of DNA are derived from its interaction with cells thatinternalize DNA. Cytokines can be released from cells that bind and/orinternalize DNA in the absence of gene transcription. Separately,interaction of antigen with APC followed by presentation and specificrecognition also stimulates release of cytokines that have positivefeedback effects on these cells and other immune cells. Chief amongthese effects are the direction of CD4⁺ T_(H) cells todifferentiate/proliferate preferentially to T_(H)1 or T_(H)2 phenotypes.Furthermore, cytokines released at the site of DNA vaccination,regardless of the mechanism of their release, contribute to recruitmentof other immune cells from the immediate local area and more distantsites such as draining lymph nodes. In recognition of the importance ofcytokines in elicitation of a potent immune response, some investigatorshave included the genes for one or more cytokines in the DNA vaccineplasmid along with the target antigen for immunization. In this casecytokines are derived not only from processes intrinsic to theinteraction of DNA with cells, or specific cell responses to theantigen, but via synthesis directed by the vaccine plasmid.

Movement of Immune Cells from the Blood Stream and Different Sites tothe Site of Immunization and Also from the Site of Immunization to OtherSites

Immune cells are recruited to the site of immunization from distantsites or the bloodstream. Specific and non-specific immune responses arethen greatly amplified. Immune cells, including APC, bearing antigenfragments complexed to MHC molecules or even expressing antigen fromuptake of plasmid, also move from the immunization site to other sites(blood, hence to all tissues; lymph nodes; spleen) where additionalimmune recruitment and qualitative and quantitative development of theimmune response ensue.

Current Genetic Vaccine Vectors Employ Simple Methods for Expression ofthe Desired Antigen with Few if any Design Elements that Control thePrecise Intracellular Fate of the Antigen or the ImmunologicalConsequences of Antigen Expression

While these pathways often compete, previously available geneticvaccines have incorporated all components for influencing each of thepathways into a single polynucleotide molecule. Because separate celltypes are involved in the complex interactions required for a potentimmune response to a genetic vaccine vector, mutually incompatibleconsequences can arise from administration of a genetic vaccine that isincorporated in a single vector molecule. Current genetic vaccinevectors employ simple methods for expression of the desired antigen withfew if any design elements that control the precise intracellular fateof the antigen or the immunological consequences of antigen expression.Thus, although genetic vaccines show great promise for vaccine researchand development, the need for major improvements and several severelimitations of these technologies are apparent.

Existing Genetic Vaccine Vectors have not been Optimized for HumanTissue, Providing Low and Short-Lasting Expression of the Antigen ofInterest, with Insufficient Stability, Inducibility, or Levels ofExpression In Vivo, Among Other Things

Largely due to the lack of suitable laboratory models, none of theexisting genetic vaccine vectors have been optimized for human tissues.The existing genetic vaccine vectors typically provide low andshort-lasting expression of the antigen of interest, and even largequantities of DNA do not always result in sufficiently high expressionlevels to induce protective immune responses. Because the mechanisms ofthe vector entry into the cells and transfer into the nucleus are poorlyunderstood, virtually no attempts have been made to improve these keyproperties. Similarly, little is known about the mechanisms thatregulate the maintenance of vector functions, including gene expression.Furthermore, although there is increasing amount of data indicating thatspecific sequences alter the immunostimulatory properties of the DNA,rational engineering is a very laborious and time-consuming approachwhen using this information to generate vector backbones with improvedimmunomodulatory properties.

Moreover, presently available genetic vaccine vectors do not providesufficient stability, inducibility or levels of expression in vivo tosatisfy the desire for vaccines which can deliver booster immunizationwithout additional vaccine administration. Booster immunizations aretypically required 34 weeks after the primary injection with existinggenetic vaccines.

Therefore a need exists for improved genetic vaccine vectors andformulations, and methods for development of such vectors. The presentinvention fulfills these and other needs.

The interactions between pathogens and hosts are results of millions ofyears of evolution, during which the mammalian immune system has evolvedsophisticated means to counterattack pathogen invasions. However,bacterial and viral pathogens have simultaneously gained a number ofmechanisms to improve their virulence and survival in hosts, providing amajor challenge for vaccine research and development despite the powersof modern techniques of molecular and cellular biology. Similar to theevolution of pathogen antigens, several cancer antigens are likely tohave gained means to down regulate their immunogenicity as a mechanismto escape the host immune system.

Efficient vaccine development is also hampered by the antigenicheterogeneity of different strains of pathogens, driven in part byevolutionary forces as means for the pathogens to escape immunedefenses. Pathogens also reduce their immunogenicity by selectingantigens that are difficult to express, process and/or transport in hostcells, thereby reducing the availability of immunogenic peptides to themolecules initiating and modulating immune responses. The mechanismsassociated with these challenges are complex, multivariate and ratherpoorly characterized. Accordingly, a need exists for vaccines that caninduce a protective immune response against bacterial and viralpathogens. The present invention fulfills this and other needs.

Antigen processing and presentation is only one factor which determinesthe effectiveness of vaccination, whether performed with geneticvaccines or more classical methods. Other molecules involved indetermining vaccine effectiveness include cytokines (interleukins,interferons, chemokines, hematopoietic growth factors, tumor necrosisfactors and transforming growth factors), which are small molecularweight proteins that regulate maturation, activation, proliferation anddifferentiation of the cells of the immune system.

Characteristic features of cytokines are pleiotropy and redundancy; thatis, one cytokine often has several functions and a given function isoften mediated by more than one cytokine. In addition, several cytokineshave additive or synergistic effects with other cytokines, and a numberof cytokines also share receptor components.

Due to the complexity of the cytokine networks, studies on thephysiological significance of a given cytokine have been difficult,although recent studies using cytokine gene-deficient mice havesignificantly improved our understanding on the functions of cytokinesin vivo. In addition to soluble proteins, several membrane-boundcostimulatory molecules play a fundamental role in the regulation ofimmune responses. These molecules include CD40, CD40 ligand, CD27, CD80,CD86 and CD150 (SLAM), and they are typically expressed on lymphoidcells after activation via antigen recognition or through cell-cellinteractions.

T helper (T_(H)) cells, key regulators of the immune system, are capableof producing a large number of different cytokines, and based on theircytokine synthesis pattern T_(H) cells are divided into two subsets(Paul and Seder (1994) Cell 76: 241-251). T_(H)1 cells produce highlevels of IL-2 and IFN-K and no or minimal levels of IL-4, IL-5 andIL-13. In contrast, T_(H)2 cells produce high levels of IL-4, IL-5 andIL-13, and IL-2 and IFN-γ production is minimal or absent. T_(H)1 cellsactivate macrophages, dendritic cells and augment the cytolytic activityof CD8⁺ cytotoxic T lymphocytes and NK cells (Id.), whereas T_(H)2 cellsprovide efficient help for B cells and they also mediate allergicresponses due to the capacity of T_(H)2 cells to induce IgE isotypeswitching and differentiation of B cells into IgE secreting cell (DeVries and Punnonen (1996) In Cytokine regulation of humoral immunity:basic and clinical aspects. Eds. Snapper, C. M., John Wiley & Sons,Ltd., West Sussex, UK, p. 195-215). The exact mechanisms that regulatethe differentiation of T helper cells are not fully understood, butcytokines are believed to play a major role. IL-4 has been shown todirect T_(H)2 differentiation, whereas IL-12 induces development ofT_(H)1 cells (Paul and Seder, supra.). In addition, it has beensuggested that membrane bound costimulatory molecules, such as CD80,CD86 and CD150, can direct T_(H)1 and/or T_(H)2 development, and thesame molecules that regulate T_(H) cell differentiation also affectactivation, proliferation and differentiation of B cells intoIg-secreting plasma cells (Cocks et al. (1995) Nature 376: 260-263;Lenschow et al. (1996) Immunity 5: 285-293; Punnonen et al. (1993) Proc.Nat'l. Acad. Sci. USA 90: 3730-3734; Punnonen et al. (1997) J Exp. Med.185: 993-1004).

Studies in both man and mice have demonstrated that the cytokinesynthesis profile of T helper (T_(H)) cells plays a crucial role indetermining the outcome of several viral, bacterial and parasiticinfections. High frequency of T_(H)1 cells generally protects fromlethal infections, whereas dominant T_(H)2 phenotype often results indisseminated, chronic infections. For example, T_(H)1 phenotype isobserved in tuberculoid (resistant) form of leprosy and T_(H)2 phenotypein lepromatous, multibacillary (susceptible) lesions (Yamamura et al.(1991) Science 254: 277-279). Similarly, late-stage HIV patients haveT_(H)2-like cytokine synthesis profiles, and T_(H)1 phenotype has beenproposed to protect from AIDS (Maggi et al. (1994) J Exp. Med. 180:489-495). Furthermore, the survival from meningococcal septicemia isgenetically determined based on the capacity of peripheral bloodleukocytes to produce TNF-α and IL-10. Individuals from families withhigh production of IL-10 have increased risk of fatal meningococcaldisease, whereas members of families with high TNF-α production weremore likely to survive the infection (Westendorp et al. (1997) Lancet349: 170-173).

Cytokine treatments can dramatically influence T_(H)1/T_(H)2 celldifferentiation and macrophage activation, and thereby the outcome ofinfectious diseases. For example, BALB/c mice infected with Leishmaniamajor generally develop a disseminated fatal disease with a T_(H)2phenotype, but when treated with anti-IL-4 mAbs or IL-12, the frequencyof T_(H)1 cells in the mice increases and they are able to counteractthe pathogen invasion (Chatelain et al. (1992) J Immunol. 148:1182-1187). Similarly, IFN-γ protects mice from lethal Herpes SimplexVirus (HSV) infection, and MCP-1 prevents lethal infections byPseudomonas aeruginosa or Salmonella typhimurium. In addition, cytokinetreatments, such as recombinant IL-2, have shown beneficial effects inhuman common variable immunodeficiency (Cunningham-Rundles et al. (1994)N. Engl. J Med. 331: 918-921).

The administration of cytokines and other molecules to modulate immuneresponses in a manner most appropriate for treating a particular diseasecan provide a significant tool for the treatment of disease. However,presently available immunomodulator treatments can have severaldisadvantages, such as insufficient specific activity, induction ofimmune responses against, the immunomodulator that is administered, andother potential problems. Thus, a need exists for immunomodulators thatexhibit improved properties relative to those currently available. Thepresent invention fulfills this and other needs.

Erythrocytes infected with the malaria parasite P. falciparum disappearfrom the peripheral circulation as they mature from the ring stage totrophozoites (Bignami and Bastianeli, Reforma Medica (1889)6:1334-1335). This phenomenon, known as sequestration, results fromparasitized erythrocyte (“PE”) adherence to microvascular endothelialcells in diverse organs (Miller, Am. J. Trop. Med. Hyg. (1969)18:860-865). Sequestration is associated temporally with expression ofknob protrusions (Leech et al., J. Cell. Biol. (1984) 98:1256-1264),expression of a very large antigenically variant surface protein, calledPfEMP1 (Aley et al., J. Exp. Med. (1984) 160:1585-1590; Leech et al., J.Exp. Med. (1984) 159:1567-1575; Howard et al., Molec. Biochem.Parasitol. (1988) 27:207-223), and expression of new receptor propertieswhich mediate adherence to endothelial cells (Miller, supra; Udeinya etal., Science (1981) 213:555-557. Endothelial cell surface proteins suchas CD36, thrombospondin (TSP) and ICAM-1 have been identified as majorhost receptors for mature PE. See, e.g., Barnwell et al., J. Immunol.(1985) 135:3494-3497; Roberts et al., Nature (1985) 318:64-66; andBerendt et al., Nature (1989) 341:57-59.

PE sequestration confers unique advantages for P. falciparum parasites(Howard and Gilladoga, Blood (1989) 74:2603-2618), but also contributesdirectly to the acute pathology of P. falciparum (Miller et al., Science(1994) 264:1878-1883). Of the four human malarias, only P. falciparuminfection is associated with neurological impairment and cerebralpathology seen increasingly in severe drug-resistant malaria (Howard andGilladoga, supra).

Although the genesis of human cerebral malaria is likely due to acombination of factors including particular parasite phenotypes (Berendtet al., Parasitol. Today (1994) 10:412-414), inappropriate immuneresponses and the phenotype of endothelial cell surface molecules in thecerebral microvasculature (Pasloske and Howard, Ann. Rev. Med.(1994):283-295), adherence of PE to cerebral blood vessels andconsequent local microvascular occlusion is a major contributing factor.See, e.g., Berendt et al., supra; Patnaik et al., Am. J. Trop. Med. Hyg.(1994) 51:642-647.

The capacity of P. falciparum PE to express variant forms of PfEMP1contributes to the special virulence of this parasite. Variant parasitescan evade variant-specific antibodies elicited by earlier infections.The P. falciparum variant antigens have been defined in vitro usingantiserum prepared in Aotus monkeys infected with individual parasitestrains (Howard et al., Molec. Biochem. Parasitol. (1988) 27:207-223).Antibodies raised against a particular parasite will only react by PEagglutination, indirect immuno-fluorescence or immunoelectronmicroscopywith PE from the same strain (van Schravendijk et al., Blood (1991)78:226-236).

Such studies with PE from malaria patients in diverse geographiclocations and sera from the same or different patients confirm that PEin natural isolates express variant surface antigens and that individualpatients respond to infection by production of isolate-specificantibodies (Marsh and Howard, Science (1986) 231:150-153; Aguiar et al.,Am. J. Trop. Med. Hyg. (1992) 47:621-632; Iqbal et al., Trans. R. Soc.Trop. Med. Hyg. (1993) 87:583-588. Expression of a variant antigen on PEhas also been demonstrated in several simian, murine and human malariaspecies, including P. knowlesi (Brown and Brown, Nature (1965)208:1286-1288; Barnwell et al., Infect. Immun. (1983) 40:985-994), P.chabaudi (Gilks et al., Parasite Immunol. (1990) 12:45-64; Brannan etal., Proc. R. Soc. Lond. Biol. Sci. (1994) 256:71-75), P. fragile(Handunnetti et al., J. Exp. Mod. (1987) 165:1269-1283) and P. vivax(Mendis et al., Am. J. Txop. Med. Hyg. (1988) 38:4246). Laboratorystudies with P. knowlesi (Brown and Brown, supra; Barnwell et al.,supra) or P. falciparum (Hommel et al., J. Exp. Med. (1983)157:1137-1148) in monkeys and P. chabaudi in mice (Gilks et al., supra)confirmed that antigenic variation at the PE surface is associated withprolonged or chronic infection and the capacity to repeatedlyre-establish blood infection in previously infected animals. Studieswith cloned parasites demonstrated that antigenic variants can arisewith extraordinary frequency, e.g., 2% per generation with P. falciparum(Roberts et al., Nature (1992) 357:689-692) and 1.6% per generation withP. chabaudi (Brannan et al., supra).

PfEMP1 was identified as a ¹²⁵I-labeled, size diverse protein (200-350kD) on PE that is lacking from uninfected erythrocytes, and that is alsolabeled by biosynthetic incorporation of radiolabeled amino acids (Leechet al., J. Exp. Med. (1984) 159:1567-1575; Howard et al., Molec.Biochem. Parasitol. (1988) 27:207-223). PfEMP1 is not extracted from PEby neutral detergents such as Triton X-100 but is extracted by SDS,suggesting that it is linked to the erythrocyte cytoskeleton (Aley etal., J. Med. Exp. (1984) 160:1585-1590). After addition of excess TritonX-100, PfEMP1 is immunoreactive with appropriate serum antibodies(Howard et al., (1988), supra). Mild trypsinization of intact PE rapidlycleaves PfEMP1 from the cell surface (Leech et al., J. Exp. Mod. (1984)159:1567-1575). PfEMP1 bears antigenically diverse epitopes since it isimmunoprecipitated from particular strains of P. falciparum byantibodies from sera of Aotus monkeys infected with the same strain, butnot by antibodies from animals infected with heterologous strains(Howard et al. (1988), supra). Knobless PE derived from parasite passagein splenectomized Aotus monkeys (Aley et al., supra) do not expresssurface PfEMP1 and are not agglutinated with sera from immuneindividuals or infected monkeys (Howard et al. (1988), supra; Howard andGilladoga, Blood (1989) 74:2603-2618). In general, sera that react withthe PE surface by indirect immunofluorescence and antibody-mediated PEagglutination are the only sera to immunoprecipitate ¹²⁵I-labeled PfEMP1from any particular strain (Howard et al., (1988), supra; vanSchravendijk et al., Blood (1991) 78:226-236; Biggs et al., J. Immunol.(1992) 149:2047-2054).

The adherence of parasitized erythrocytes to endothelial cells ismediated by multiple receptor/counter-receptor interactions, includingCD36, thrombospondin and intracellular adhesion molecule-1 (ICAM-1) asthe major host cell receptors (Howard and Gilladoga, Blood (1989)74:2603-2618, Pasloske and Howard, Ann. Rev. Med. (1994) 45:283-295).

Vascular cell adhesion molecule-1 (VCAM-1) and endothelial leukocyteadhesion molecule-1 (ELAM-1) have also been implicated as additionalendothelial cell receptors that can mediate adherence of a minority ofP. falciparum PE (Ockenhouse, et al., J. Exp. Med. (1992) 176:1183-1189,and Howard and Paslaske, supra). The adherence receptors on the surfaceof PE has not yet been conclusively identified, and several molecules,including AG 332 (Udomsangpetch, et al., Nature (1989) 338:763-765),modified band 3 (Crandall, et al., Proc. Nat'l Acad. Sci. USA (1993)90:4703-4707), Sequestrin (Ockenhouse, Proc. Nat'l Acad. Sci. USA (1991)88:3175-3179), and PfEMP1 (Howard and Gilladoga, supra, and Pasloske andHoward, supra), have been proposed as candidates. Several pieces ofindirect evidence have linked expression of PfEMP1 with the acquisitionof new host protein receptor properties on the surface of PE (Howard andGilladoga, supra; Pasloske and Howard, Ann. Rev. Med. (1994)45:283-295). PE adherence is correlated with the expression of PfEMP1 onthe surface of mature stage PE (Leech, et al., J. Exp. Med. (1984)159:1567-1575). Alterations in the adherence phenotype of the PEselected for in vitro are usually associated with the emergence of newforms of PfEMP1 (Biggs, et al., J. Immunol. (1992) 149:2047-2054;Roberts, et al., Nature (1992) 357:689-692). Mild trypsinization ofintact mature PE cleaves the extracellular portion of PfEMP1 and at thesame time, reduces or eliminates PE cytoadherence (Leech, et al., supra)Previously described antibody mediated blockade or reversal ofcytoadherence is strain specific and is correlated with the ability ofthe reacting sera to agglutinate the corresponding PE and toimmunoprecipitate the surface labeled ¹²⁵I-PfEMP1 (Howard, et al.,Molec. Biochem. Parasitol. (1988) 27:207-224). Pfalhesin (modified band3) have been shown to bind CD36 under non-physiological conditions(Crandall, et al., Exp. Parasitol. (1994) 78:203-209). Sequestrin, whichappears to be homologous to PfEMP1, extracted with TX100 from knoblessPE, was shown to bind to immobilized CD36 (Ockenhouse, Proc. Nat'l Acad.Sci. USA (1991) 88:3175-3179).

The complex nature and/or mechanism of malarial antigenic variation, andits particular virulence has created a need for methods and compositionswhich may be useful in the treatment diagnosis and prevention of malariainfections. The present invention meets these and other needs.

General Overview of Problems & Considerations in Directed Evolution

The approach, termed directed evolution, of experimentally modifying abiological molecule towards a desirable property, can be achieved bymutagenizing one or more parental molecular templates and by identifyingany desirable molecules among the progeny molecules. Currently availabletechnologies in directed evolution include methods for achievingstochastic (i.e. random) mutagenesis and methods for achievingnon-stochastic (non-random) mutagenesis. However, critical shortfalls inboth types of methods are identified in the instant disclosure.

In prelude, it is noteworthy that it may be argued philosophically bysome that all mutagenesis—if considered from an objective point ofview—is non-stochastic; and furthermore that the entire universe isundergoing a process that—if considered from an objective point ofview—is non-stochastic. Whether this is true is outside of the scope ofthe instant consideration. Accordingly, as used herein, the terms“randomness”, “uncertainty”, and “unpredictability” have subjectivemeanings, and the knowledge, particularly the predictive knowledge, ofthe designer of an experimental process is a determinant of whether theprocess is stochastic or non-stochastic.

By way of illustration, stochastic or random mutagenesis is exemplifiedby a situation in which a progenitor molecular template is mutated(modified or changed) to yield a set of progeny molecules havingmutation(s) that are not predetermined. Thus, in an in vitro stochasticmutagenesis reaction, for example, there is not a particularpredetermined product whose production is intended; rather there is anuncertainty—hence randomness—regarding the exact nature of the mutationsachieved, and thus also regarding the products generated. In contrast,non-stochastic or non-random mutagenesis is exemplified by a situationin which a progenitor molecular template is mutated (modified orchanged) to yield a progeny molecule having one or more predeterminedmutations. It is appreciated that the presence of background products insome quantity is a reality in many reactions where molecular processingoccurs, and the presence of these background products does not detractfrom the non-stochastic nature of a mutagenesis process having apredetermined product.

Thus, as used herein, stochastic mutagenesis is manifested in processessuch as error-prone PCR and stochastic shuffling, where the mutation(s)achieved are random or not predetermined. In contrast, as used herein,non-stochastic mutagenesis is manifested in instantly disclosedprocesses such as gene site-saturation mutagenesis and syntheticligation reassembly, where the exact chemical structure(s) of theintended product(s) are predetermined.

In brief, existing mutagenesis methods that are non-stochastic have beenserviceable in generating from one to only a very small number ofpredetermined mutations per method application, and thus produce permethod application from one to only a few progeny molecules that havepredetermined molecular structures. Moreover, the types of mutationscurrently available by the application of these non-stochastic methodsare also limited, and thus so are the types of progeny mutant molecules.

In contrast, existing methods for mutagenesis that are stochastic innature have been serviceable for generating somewhat larger numbers ofmutations per method application—though in a random fashion & usuallywith a large but unavoidable contingency of undesirable backgroundproducts. Thus, these existing stochastic methods can produce per methodapplication larger numbers of progeny molecules, but that haveundetermined molecular structures. The types of mutations that can beachieved by application of these current stochastic methods are alsolimited, and thus so are the types of progeny mutant molecules.

It is instantly appreciated that there is a need for the development ofnon-stochastic mutagenesis methods that:

1) Can be used to generate large numbers of progeny molecules that havepredetermined molecular structures;

2) Can be used to readily generate more types of mutations;

3) Can produce a correspondingly larger variety of progeny mutantmolecules;

4) Produce decreased unwanted background products;

5) Can be used in a manner that is exhaustive of all possibilities; and

6) Can produce progeny molecules in a systematic & non-repetitive way.

The instant invention satisfies all of these needs.

Directed Evolution Supplements Natural Evolution: Natural evolution hasbeen a springboard for directed or experimental evolution, serving bothas a reservoir of methods to be mimicked and of molecular templates tobe mutagenized. It is appreciated that, despite its intrinsicprocess-related limitations (in the types of favored &/or allowedmutagenesis processes) and in its speed, natural evolution has had theadvantage of having been in process for millions of years and throughouta wide diversity of environments. Accordingly, natural evolution(molecular mutagenesis and selection in nature) has resulted in thegeneration of a wealth of biological compounds that have shownusefulness in certain commercial applications.

However, it is instantly appreciated that many unmet commercial needsare discordant with any evolutionary pressure &/or direction that can befound in nature. Moreover, it is often the case that when commerciallyuseful mutations would otherwise be favored at the molecular level innature, natural evolution often overrides the positive selection of suchmutations, e.g. when there is a concurrent detriment to an organism as awhole (such as when a favorable mutation is accompanied by a detrimentalmutation). Additionally, natural evolution is often slow, and favorsfidelity in many types of replication. Additionally still, naturalevolution often favors a path paved mainly by consecutive beneficialmutations while tending to avoid a plurality of successive negativemutations, even though such negative mutations may prove beneficial whencombined, or may lead—through a circuitous route—to final state that isbeneficial.

Moreover, natural evolution advances through specific steps (e.g.specific mutagenesis and selection processes), with avoidance of lessfavored steps. For example, many nucleic acids do not reach close enoughproximity to each other in a operative environment to undergochimerization or incorporation or other types of transfers from onespecies to another. Thus, e.g., when sexual intercourse between 2particular species is avoided in nature, the chimerization of nucleicacids from these 2 species is likewise unlikely, with parasites commonto the two species serving as an example of a very slow passageway forinter-molecular encounters and exchanges of DNA. For another example,the generation of a molecule causing self-toxicity or self-lethality orsexual sterility is avoided in nature. For yet another example, thepropagation of a molecule having no particular immediate benefit to anorganism is prone to vanish in subsequent generations of the organism.Furthermore, e.g., there is no selection pressure for improving theperformance of molecule under conditions other than those to which it isexposed in its endogenous environment; e.g. a cytoplasmic molecule isnot likely to acquire functional features extending beyond what isrequired of it in the cytoplasm. Furthermore still, the propagation of abiological molecule is susceptible to any global detrimentaleffects—whether caused by itself or not—on its ecosystem. These andother characteristics greatly limit the types of mutations that can bepropagated in nature.

On the other hand, directed (or experimental) evolution—particularly asprovided herein—can be performed much more rapidly and can be directedin a more streamlined manner at evolving a predetermined molecularproperty that is commercially desirable where nature does not provideone &/or is not likely to provide. Moreover, the directed evolutioninvention provided herein can provide more wide-ranging possibilities inthe types of steps that can be used in mutagenesis and selectionprocesses. Accordingly, using templates harvested from nature, theinstant directed evolution invention provides more wide-rangingpossibilities in the types of progeny molecules that can be generatedand in the speed at which they can be generated than often nature itselfmight be expected to in the same length of time.

In a particular exemplification, the instantly disclosed directedevolution methods can be applied iteratively to produce a lineage ofprogeny molecules (e.g. comprising successive sets of progeny molecules)that would not likely be propagated (i.e., generated &/or selected for)in nature, but that could lead to the generation of a desirabledownstream mutagenesis product that is not achievable by naturalevolution.

Previous Directed Evolution Methods are Suboptimal:

Mutagenesis has been attempted in the past on many occasions, but bymethods that are inadequate for the purpose of this invention. Forexample, previously described non-stochastic methods have beenserviceable in the generation of only very small sets of progenymolecules (comprised often of merely a solitary progeny molecule). Byway of illustration, a chimeric gene has been made by joining 2polynucleotide fragments using compatible sticky ends generated byrestriction enzyme(s), where each fragment is derived from a separateprogenitor (or parental) molecule. Another example might be themutagenesis of a single codon position (i.e. to achieve a codonsubstitution, addition, or deletion) in a parental polynucleotide togenerate a single progeny polynucleotide encoding for a singlesite-mutagenized polypeptide.

Previous non-stochastic approaches have only been serviceable in thegeneration of but one to a few mutations per method application. Thus,these previously described non-stochastic methods thus fail to addressone of the central goals of this invention, namely the exhaustive andnon-stochastic chimerization of nucleic acids. Accordingly previousnon-stochastic methods leave untapped the vast majority of the possiblepoint mutations, chimerizations, and combinations thereof, which maylead to the generation of highly desirable progeny molecules.

In contrast, stochastic methods have been used to achieve larger numbersof point mutations and/or chimerizations than non-stochastic methods;for this reason, stochastic methods have comprised the predominantapproach for generating a set of progeny molecules that can be subjectedto screening, and amongst which a desirable molecular species mighthopefully be found. However, a major drawback of these approaches isthat—because of their stochastic nature—there is a randomness to theexact components in each set of progeny molecules that is produced.Accordingly, the experimentalist typically has little or no idea whatexact progeny molecular species are represented in a particular reactionvessel prior to their generation. Thus, when a stochastic procedure isrepeated (e.g. in a continuation of a search for a desirable progenymolecule), the re-generation and re-screening of previously discardedundesirable molecular species becomes a labor-intensive obstruction toprogress, causing a circuitous—if not circular—path to be taken. Thedrawbacks of such a highly suboptimal path can be addressed bysubjecting a stochastically generated set of progeny molecules to alabor-incurring process, such as sequencing, in order to identify theirmolecular structures, but even this is an incomplete remedy.

Moreover, current stochastic approaches are highly unsuitable forcomprehensively or exhaustively generating all the molecular specieswithin a particular grouping of mutations, for attributing functionalityto specific structural groups in a template molecule (e.g. a specificsingle amino acid position or a sequence comprised of two or more aminoacids positions), and for categorizing and comparing specific groupingof mutations. Accordingly, current stochastic approaches do notinherently enable the systematic elimination of unwanted mutagenesisresults, and are, in sum, burdened by too many inherently shortcomingsto be optimal for directed evolution.

In a non-limiting aspect, the instant invention addresses these problemsby providing non-stochastic means for comprehensively and exhaustivelygenerating all possible point mutations in a parental template. Inanother non-limiting aspect, the instant invention further providesmeans for exhaustively generating all possible chimerizations within agroup of chimerizations. Thus, the aforementioned problems are solved bythe instant invention.

Specific shortfalls in the technological landscape addressed by thisinvention include:

1) Site-directed mutagenesis technologies, such as sloppy orlow-fidelity PCR, are ineffective for systematically achieving at eachposition (site) along a polypeptide sequence the full (saturated) rangeof possible mutations (i.e. all possible amino acid substitutions).

2) There is no relatively easy systematic means for rapidly analyzingthe large amount of information that can be contained in a molecularsequence and in the potentially colossal number or progeny moleculesthat could be conceivably obtained by the directed evolution of one ormore molecular templates.

3) There is no relatively easy systematic means for providingcomprehensive empirical information relating structure to function formolecular positions.

4) There is no easy systematic means for incorporating internalcontrols, such as positive controls, for key steps in certainmutagenesis (e.g. chimerization) procedures.

5) There is no easy systematic means to select for a specific group ofprogeny molecules, such as full-length chimeras, from among smallerpartial sequences.

An exceedingly large number of possibilities exist for the purposefuland random combination of amino acids within a protein to produce usefulhybrid proteins and their corresponding biological molecules encodingfor these hybrid proteins, i.e., DNA, RNA. Accordingly, there is a needto produce and screen a wide variety of such hybrid proteins for adesirable utility, particularly widely varying random proteins.

The complexity of an active sequence of a biological macromolecule(e.g., polynucleotides, polypeptides, and molecules that are comprisedof both polynucleotide and polypeptide sequences) has been called itsinformation content (“IC”), which has been defined as the resistance ofthe active protein to amino acid sequence variation (calculated from theminimum number of invariable amino acids (bits) required to describe afamily of related sequences with the same function). Proteins that aremore sensitive to random mutagenesis have a high information content.

Molecular biology developments, such as molecular libraries, haveallowed the identification of quite a large number of variable bases,and even provide ways to select functional sequences from randomlibraries. In such libraries, most residues can be varied (althoughtypically not all at the same time) depending on compensating changes inthe context. Thus, while a 100 amino acid protein can contain only 2,000different mutations, 20¹⁰⁰ sequence combinations are possible.

Information density is the IC per unit length of a sequence. Activesites of enzymes tend to have a high information density. By contrast,flexible linkers of information in enzymes have a low informationdensity.

Current methods in widespread use for creating alternative proteins in alibrary format are error-prone polymerase chain reactions and cassettemutagenesis, in which the specific region to be optimized is replacedwith a synthetically mutagenized oligonucleotide. In both cases, asubstantial number of mutant sites are generated around certain sites inthe original sequence.

Error-prone PCR uses low-fidelity polymerization conditions to introducea low level of point mutations randomly over a long sequence. In amixture of fragments of unknown sequence, error-prone PCR can be used tomutagenize the mixture. The published error-prone PCR protocols sufferfrom a low processivity of the polymerase. Therefore, the protocol isunable to result in the random mutagenesis of an average-sized gene.This inability limits the practical application of error-prone PCR. Somecomputer simulations have suggested that point mutagenesis alone mayoften be too gradual to allow the large-scale block changes that arerequired for continued and dramatic sequence evolution. Further, thepublished error-prone PCR protocols do not allow for amplification ofDNA fragments greater than 0.5 to 1.0 kb, limiting their practicalapplication. In addition, repeated cycles of error-prone PCR can lead toan accumulation of neutral mutations with undesired results, such asaffecting a protein's immunogenicity but not its binding affinity.

In oligonucleotide-directed mutagenesis, a short sequence is replacedwith a synthetically mutagenized oligonucleotide. This approach does notgenerate combinations of distant mutations and is thus notcombinatorial. The limited library size relative to the vast sequencelength means that many rounds of selection are unavoidable for proteinoptimization. Mutagenesis with synthetic oligonucleotides requiressequencing of individual clones after each selection round followed bygrouping them into families, arbitrarily choosing a single family, andreducing it to a consensus motif. Such motif is re-synthesized andreinserted into a single gene followed by additional selection. Thisstep process constitutes a statistical bottleneck, is labor intensive,and is not practical for many rounds of mutagenesis.

Error-prone PCR and oligonucleotide-directed mutagenesis are thus usefulfor single cycles of sequence fine tuning, but rapidly become toolimiting when they are applied for multiple cycles.

Another limitation of error-prone PCR is that the rate of down-mutationsgrows with the information content of the sequence. As the informationcontent, library size, and mutagenesis rate increase, the balance ofdown-mutations to up-mutations will statistically prevent the selectionof further improvements (statistical ceiling).

In cassette mutagenesis, a sequence block of a single template istypically replaced by a (partially) randomized sequence. Therefore, themaximum information content that can be obtained is statisticallylimited by the number of random sequences (i.e., library size). Thiseliminates other sequence families which are not currently best, butwhich may have greater long term potential.

Also, mutagenesis with synthetic oligonucleotides requires sequencing ofindividual clones after each selection round. Thus, such an approach istedious and impractical for many rounds of mutagenesis.

Thus, error-prone PCR and cassette mutagenesis are best suited, and havebeen widely used, for fine-tuning areas of comparatively low informationcontent. One apparent exception is the selection of an RNA ligaseribozyme from a random library using many rounds of amplification byerror-prone PCR and selection.

In nature, the evolution of most organisms occurs by natural selectionand sexual reproduction. Sexual reproduction ensures mixing andcombining of the genes in the offspring of the selected individuals.During meiosis, homologous chromosomes from the parents line up with oneanother and cross-over part way along their length, thus randomlyswapping genetic material. Such swapping or shuffling of the DNA allowsorganisms to evolve more rapidly.

In recombination, because the inserted sequences were of proven utilityin a homologous environment, the inserted sequences are likely to stillhave substantial information content once they are inserted into the newsequence.

Theoretically there are 2,000 different single mutants of a 100 aminoacid protein. However, a protein of 100 amino acids has 20¹⁰⁰ possiblesequence combinations, a number which is too large to exhaustivelyexplore by conventional methods. It would be advantageous to develop asystem which would allow generation and screening of all of thesepossible combination mutations.

Some workers in the art have utilized an in vivo site specificrecombination system to generate hybrids of combine light chain antibodygenes with heavy chain antibody genes for expression in a phage system.However, their system relies on specific sites of recombination and islimited accordingly. Simultaneous mutagenesis of antibody CDR regions insingle chain antibodies (scFv) by overlapping extension and PCR havebeen reported.

Others have described a method for generating a large population ofmultiple hybrids using random in vivo recombination. This methodrequires the recombination of two different libraries of plasmids, eachlibrary having a different selectable marker. The method is limited to afinite number of recombinations equal to the number of selectablemarkers existing, and produces a concomitant linear increase in thenumber of marker genes linked to the selected sequence(s).

In vivo recombination between two homologous, but truncated,insect-toxin genes on a plasmid has been reported as a method ofproducing a hybrid gene. The in vivo recombination of substantiallymismatched DNA sequences in a host cell having defective mismatch repairenzymes, resulting in hybrid molecule formation has been reported.

1.3. Summary of the Invention Directing an Immune Response so as toAchieve an Optimal Response to Vaccination.

The present invention provides multicomponent genetic vaccines thatinclude at least one, and preferably two or more genetic vaccinecomponents that confer upon the vaccine the ability to direct an immuneresponse so as to achieve an optimal response to vaccination. Forexample, the genetic vaccines can include a component that providesoptimal antigen release; a component that provides optimal production ofcytotoxic T lymphocytes; a component that directs release of animmunomodulator; a component that directs release of a chemokine; and/ora component that facilitates binding to, or entry into, a desired targetcell type. For example, a component can confer improved binding to, anduptake of, the genetic vaccine to target cells such asantigen-expressing cells or antigen-presenting cells.

Additional components include those that direct antigen peptides derivedfrom uptake of an antigen into a cell to presentation on either Class Ior Class II molecules. For example, one can include a component thatdirects antigen peptides to presentation on Class I molecules andcomprises a polynucleotide that encodes a protein such as tapasin, TAP-1and TAP-2, and/or a component that directs antigen peptides topresentation on Class II molecules and comprises a polynucleotide thatencodes a protein such as an endosomal or lysosomal protease.

In a particularly preferred aspect, this invention provides a method forobtaining an immunomodulatory polynucleotide that has an optimizedmodulatory effect on an immune response, or encodes a polypeptide thathas an optimized modulatory effect on an immune response, the methodcomprising: creating a library of non-stochastically generated progenypolynucleotides from a parental polynucleotide set; wherein optimizationcan thus be achieved using one or more of the directed evolution methodsas described herein in any combination, permutation and iterativemanner; whereby these directed evolution methods include theintroduction of mutations by non-stochastic methods, including by “genesite saturation mutagenesis” as described herein; and whereby thesedirected evolution methods also include the introduction mutations bynon-stochastic polynucleotide reassembly methods as described herein;including by synthetic ligation polynucleotide reassembly as describedherein.

In another particularly preferred aspect, this invention provides amethod for obtaining an immunomodulatory polynucleotide that has anoptimized modulatory effect on an immune response, or encodes apolypeptide that has an optimized modulatory effect on an immuneresponse, the method comprising:

screening a library of non-stochastically generated progenypolynucleotides to identify an optimized non-stochastically generatedprogeny polynucleotide that has, or encodes a polypeptide that has, amodulatory effect on an immune response; wherein the optimizednon-stochastically generated polynucleotide or the polypeptide encodedby the non-stochastically generated polynucleotide exhibits an enhancedability to modulate an immune response compared to a parentalpolynucleotide from which the library was created.

In another particularly preferred aspect, this invention provides amethod for obtaining an immunomodulatory polynucleotide that has anoptimized modulatory effect on an immune response, or encodes apolypeptide that has an optimized modulatory effect on an immuneresponse, the method comprising: a) creating a library ofnon-stochastically generated progeny polynucleotides from a parentalpolynucleotide set; and b) screening the library to identify anoptimized non-stochastically generated progeny polynucleotide that has,or encodes a polypeptide that has, a modulatory effect on an immuneresponse induced by a genetic vaccine vector; wherein the optimizednon-stochastically generated polynucleotide or the polypeptide encodedby the non-stochastically generated polynucleotide exhibits an enhancedability to modulate an immune response compared to a parentalpolynucleotide from which the library was created; whereby optimizationcan thus be achieved using one or more of the directed evolution methodsas described herein in any combination, permutation, and iterativemanner; whereby these directed evolution methods include theintroduction of point mutations by non-stochastic methods, including by“gene site saturation mutagenesis” as described herein; and wherebythese directed evolution methods also include the introduction mutationsby non-stochastic polynucleotide reassembly methods as described herein;including by synthetic ligation polynucleotide reassembly as describedherein.

In another particularly preferred aspect, this invention provides amethod for obtaining an immunomodulatory polynucleotide that has, anoptimized expression in a recombinant expression host, the methodcomprising: creating a library of non-stochastically generated progenypolynucleotides from a parental polynucleotide set; whereby optimizationcan thus be achieved using one or more of the directed evolution methodsas described herein in any combination, permutation and iterativemanner; whereby these directed evolution methods include theintroduction of mutations by non-stochastic methods, including by “genesite saturation mutagenesis” as described herein; and whereby thesedirected evolution methods also include the introduction mutations bynon-stochastic polynucleotide reassembly methods as described herein;including by synthetic ligation polynucleotide reassembly as describedherein.

In another particularly preferred aspect, this invention provides amethod for obtaining an immunomodulatory polynucleotide that has anoptimized expression in a recombinant expression host, the methodcomprising: screening a library of non-stochastically generated progenypolynucleotides to identify an optimized non-stochastically generatedprogeny polynucleotide that has an optimized expression in a recombinantexpression host when compared to the expression of a parentalpolynucleotide from which the library was created.

In another particularly preferred aspect, this invention provides amethod for obtaining an immunomodulatory polynucleotide that has anoptimized expression in a recombinant expression host, the methodcomprising: a) creating a library of non-stochastically generatedprogeny polynucleotides from a parental polynucleotide set; and b)screening a library of non-stochastically generated progenypolynucleotides to identify an optimized non-stochastically generatedprogeny polynucleotide that has an optimized expression in a recombinantexpression host when compared to the expression of a parentalpolynucleotide from which the library was created; whereby optimizationcan thus be achieved using one or more of the directed evolution methodsas described herein in any combination, permutation, and iterativemanner; whereby these directed evolution methods include theintroduction of point mutations by non-stochastic methods, including by“gene site saturation mutagenesis” as described herein; and wherebythese directed evolution methods also include the introduction mutationsby non-stochastic polynucleotide reassembly methods as described herein;including by synthetic ligation polynucleotide reassembly as describedherein.

In one aspect, this invention provides that the ability to a vaccine,for example a genetic vaccine, or a component of a vaccine, for examplea component of a genetic vaccine by optimizing its immunogenicity.Moreover, the present invention provides for the modification of otherproperties, including its:

-   -   Catalysed reaction(s)    -   Reaction type    -   Natural substrate(s)    -   Substrate spectrum    -   Product spectrum    -   Inhibitor(s)    -   Cofactor(s)/prostetic group(s)    -   Metal compounds/salts that affect it    -   Turnover number    -   Specific activity    -   Km value    -   pH optimum    -   pH range    -   Temperature optimum    -   Temperature range

It is also instantly appreciated that the serviceability of a moleculewith an immunogenic effect can be affected by additional physicalproperties, which can likewise be modified by directed evolution asprovided herein, such as how it is affected by subjection to:

-   -   Isolation/Preparation    -   Purification    -   Renaturating conditions (reversibility or retention of activity        upon: heating and cooling, urea, salts, detergents, pH extremes)    -   Crystallization    -   pH    -   Temperature    -   Oxidation    -   Organic solvent(s)    -   Miscellaneous storage conditions

Moreover, the instant invention provides for the modification ofmolecule's immunogenic properties such as

-   -   Exposure to biological compartments (stomach acids, in vivo        degradation)    -   Expression (e.g. Transcription &/or Translation) level    -   mRNA stability    -   Any in vivo interactions with other cells or biologicals

Method for Obtaining the Genetic Components.

In some embodiments, one or more of the genetic vaccine components isobtained by a method that involves: (1) reassembling (&/or subjecting toone or more directed evolution methods described herein) at least firstand second forms of a nucleic acid which can confer a desired propertyupon a genetic vaccine, wherein the first and second forms differ fromeach other in two or more nucleotides, to produce a library ofrecombinant nucleic acids; and (2) screening the library to identify atleast one optimized recombinant component that exhibits an enhancedcapacity to confer the desired property upon the genetic vaccine. Iffurther optimization of the component is desired, the followingadditional steps can be conducted: (3) reassembling (&/or subjecting toone or more directed evolution methods described herein) at least oneoptimized recombinant component with a further form of the nucleic acid,which is the same or different from the first and second forms, toproduce a further library of recombinant nucleic acids; (4) screeningthe further library to identify at least one further optimizedrecombinant component that exhibits an enhanced capacity to confer thedesired property upon the genetic vaccine; and (5) repeating (3) and(4), as necessary, until the further optimized recombinant componentexhibits a further enhanced capacity to confer the desired property uponthe genetic vaccine.

Members of a Gene Family

In some embodiments of the invention, the first form of the nucleic acidis a first member of a gene family and the second form of the nucleicacid comprises a second member of the gene family. Additional forms ofthe module nucleic acid can also be members of the gene family. As anexample, the first member of the gene family can be obtained from afirst species of organism and the second member of the gene familyobtained from a second species of organism. If desired, the optimizedrecombinant genetic vaccine component obtained by the methods of theinvention can be backcrossed by, for example, reassembling (&/orsubjecting to one or more directed evolution methods described herein)the optimized recombinant genetic vaccine component with a molar excessof one or both of the first and second forms of the substrate nucleicacids to produce a further library of recombinant genetic vaccinecomponents; and screening the further library to identify at least oneoptimized recombinant genetic vaccine component that further enhancesthe capability of a genetic vaccine vector that includes the componentto modulate the immune response.

Methods of Obtaining a Genetic Vaccine Component that Confers upon aGenetic Vaccine Vector an Enhanced Ability to Replicate in a Host Cell.

Additional embodiments of the invention provide methods of obtaining agenetic vaccine component that confers upon a genetic vaccine vector anenhanced ability to replicate in a host cell. These methods involvecreating a library of recombinant nucleic acids by subjecting toreassembly (&/or one or more additional directed evolution methodsdescribed herein) at least two forms of a polynucleotide that can conferepisomal replication upon a vector that contains the polynucleotide;introducing into a population of host cells a library of vectors, eachof which contains a member of the library of recombinant nucleic acidsand a polynucleotide that encodes a cell surface antigen; propagatingthe population of host cells for multiple generations; and identifyingcells which display the cell surface antigen on a surface of the cell,wherein cells which display the cell surface antigen are likely toharbor a vector that contains a recombinant vector module which enhancesthe ability of the vector to replicate episomally.

Obtaining Genetic Vaccine Components that Confer upon a Vector anEnhanced Ability to Replicate in a Host Cell.

Genetic vaccine components that confer upon a vector an enhanced abilityto replicate in a host cell can also be obtained by creating a libraryof recombinant nucleic acids by subjecting to reassembly (&/or one ormore additional directed evolution methods described herein) at leasttwo forms of a polynucleotide derived from a human papillomavirus thatcan confer episomal replication upon a vector that contains thepolynucleotide; introducing a library of vectors, each of which containsa member of the library of recombinant nucleic acids, into a populationof host cells; propagating the host cells for a plurality ofgenerations; and identifying cells that contain the vector.

In additional embodiments, the invention provides methods obtaining agenetic vaccine component that confers upon a vector an enhanced abilityto replicate in a human host cell by creating a library of recombinantnucleic acids by subjecting to reassembly (&/or one or more additionaldirected evolution methods described herein) at least two forms of apolynucleotide that can confer episomal replication upon a vector thatcontains the polynucleotide; introducing a library of genetic vaccinevectors, each of which comprises a member of the library of recombinantnucleic acids, into a test system that mimics a human immune response;and determining whether the genetic vaccine vector replicates or inducesan immune response in the test system. A suitable test system caninvolve human skin cells present as a xenotransplant on skin of animmunocompromised non-human host animal, for example, or a non-humanmammal that comprises a functional human immune system. Replication inthese systems can be detected by determining whether the animal exhibitsan immune response against the antigen.

The invention also provides methods of obtaining a genetic vaccinecomponent that confers upon a genetic vaccine an enhanced ability toenter an antigen-presenting cell. These methods involve creating alibrary of recombinant nucleic acids by subjecting to reassembly (&/orone or more additional directed evolution methods described herein) atleast two forms of a polynucleotide that can confer episomal replicationupon a vector that contains the polynucleotide; introducing a library ofgenetic vaccine vectors, each of which comprises a member of the libraryof recombinant nucleic acids, into a population of antigen-presenting orantigen-processing cells; and determining the percentage of cells in thepopulation which contain the nucleic acid vector. Antigen-presenting orantigen-processing cells of interest include, for example, B cells,monocytes/macrophages, dendritic cells, Langerhans cells, keratinocytes,and muscle cells.

The present invention provides methods of obtaining a polynucleotidethat has a modulatory effect on an immune response that is induced by agenetic vaccine, either directly (i.e., as an immunomodulatorypolynucleotide) or indirectly (i.e., upon translation of thepolynucleotide to create an immunomodulatory polypeptide. The methods ofthe invention involve: creating a library of experimentally generated(in vitro &/or in vivo) polynucleotides; and screening the library toidentify at least one optimized experimentally generated (in vitro &/orin vivo) polynucleotide that exhibits, either by itself or through theencoded polypeptide, an enhanced ability to modulate an immune responsethan a form of the nucleic acid from which the library was created.Examples include, for example, CpG-rich polynucleotide sequences,polynucleotide sequences that encode a costimulator (e.g., B7-1, B7-2,CD1, CD40, CD154 (ligand for CD40), CD150 (SLAM), or a cytokine. Thescreening step used in these methods can include, for example,introducing genetic vaccine vectors which comprise the library ofrecombinant nucleic acids into a cell, and identifying cells whichexhibit an increased ability to modulate an immune response of interestor increased ability to express an immunomodulatory molecule. Forexample, a library of recombinant cytokine-encoding nucleic acids can bescreened by testing the ability of cytokines encoded by the nucleicacids to activate cells which contain a receptor for the cytokine. Thereceptor for the cytokine can be native to the cell, or can be expressedfrom a heterologous nucleic acid that encodes the cytokine receptor. Forexample, the optimized costimulators can be tested to identify those forwhich the cells or culture medium are capable of inducing apredominantly T_(H)2 immune response, or a predominantly T_(H)1 immuneresponse.

In some embodiments, the polynucleotide that has a modulatory effect onan immune response is obtained by: (1) reassembling (&/or subjecting toone or more directed evolution methods described herein) at least firstand second forms of a nucleic acid that is, or encodes a molecule thatis, involved in modulating an immune response, wherein the first andsecond forms differ from each other in two or more nucleotides, toproduce a library of experimentally generated (in vitro &/or in vivo)polynucleotides; and (2) screening the library to identify at least oneoptimized experimentally generated (in vitro &/or in vivo)polynucleotide that exhibits, either by itself or through the encodedpolypeptide, an enhanced ability to modulate an immune response than aform of the nucleic acid from which the library was created. Ifadditional optimization is desired, the method can further involve: (3)reassembling (&/or subjecting to one or more directed evolution methodsdescribed herein) at least one optimized experimentally generated (invitro &/or in vivo) polynucleotide with a further form of the nucleicacid, which is the same or different from the first and second forms, toproduce a further library of experimentally generated (in vitro &/or invivo) polynucleotides; (4) screening, the further library to identify atleast one further optimized experimentally generated (in vitro &/or invivo) polynucleotide that exhibits an enhanced ability to modulate animmune response than a form of the nucleic acid from which the librarywas created; and (5) repeating (3) and (4), as necessary, until thefurther optimized experimentally generated (in vitro &/or in vivo)polynucleotide exhibits an further enhanced ability to modulate animmune response than a form of the nucleic acid from which the librarywas created.

In some embodiments of the invention, the library of experimentallygenerated (in vitro &/or in vivo) polynucleotides is screened by:expressing the experimentally generated (in vitro &/or in vivo)polynucleotides so that the encoded peptides or polypeptides areproduced as fusions with a protein displayed on the surface of areplicable genetic package; contacting the replicable genetic packageswith a plurality of cells that display the receptor; and identifyingcells that exhibit a modulation of an immune response mediated by thereceptor.

The invention also provides methods for obtaining a polynucleotide thatencodes an accessory molecule that improves the transport orpresentation of antigens by a cell. These methods involve creating alibrary of experimentally generated (in vitro &/or in vivo)polynucleotides by subjecting to reassembly (&/or one or more additionaldirected evolution methods described herein) nucleic acids that encodeall or part of the accessory molecule; and screening the library toidentify an optimized experimentally generated (in vitro &/or in vivo)polynucleotide that encodes a recombinant accessory molecule thatconfers upon a cell an increased or decreased ability to transport orpresent an antigen on a surface of the cell compared to an accessorymolecule encoded by the non-recombinant nucleic acids. In someembodiments, the screening step involves: introducing the library ofexperimentally generated (in vitro &/or in vivo) polynucleotides into agenetic vaccine vector that encodes an antigen to form a library ofvectors; introducing the library of vectors into mammalian cells; andidentifying mammalian cells that exhibit increased or decreasedimmunogenicity to the antigen.

In some embodiments of the invention, the cytokine that is optimized isinterleukin-12 and the screening is performed by growing mammalian cellswhich contain the genetic vaccine vector in a culture medium, anddetecting whether T cell proliferation or T cell differentiation isinduced by contact with the culture medium. In another embodiment, thecytokine is interferon-K and the screening is performed by expressingthe recombinant vector module as a fusion protein which is displayed onthe surface of a bacteriophage to form a phage display library, andidentifying phage library members which are capable of inhibitingproliferation of a B cell line. Another embodiment utilizes B7-1 (CD80)or B7-2 (CD86) as the costimulator and the cell or culture medium istested for ability to modulate an immune response.

The invention provides methods of using stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly to obtain optimized recombinant vector modules that encodecytokines and other costimulators that exhibit reduced immunogenicitycompared to a corresponding polypeptide encoded by a non-optimizedvector module. The reduced immunogenicity can be detected by introducinga cytokine or costimulator encoded by the recombinant vector module intoa mammal and determining whether an immune response is induced againstthe cytokine.

The invention also provides methods of obtaining optimizedimmunomodulatory sequences that encode a cytokine antagonist. Forexample, suitable cytokine agonists include a soluble cytokine receptorand a transmembrane cytokine receptor having, a defective signalsequence. Examples include sIL-10R and sIL-4R, and the like.

The present invention provides methods for obtaining a cell-specificbinding molecule that is useful for increasing uptake or specificity ofa genetic vaccine to a target cell. The methods involve: creating alibrary of experimentally generated (in vitro &/or in vivo)polynucleotides that by reassembling (&/or subjecting to one or moredirected evolution methods described herein) a nucleic acid that encodesa polypeptide that comprises a nucleic acid binding domain and a nucleicacid that encodes a polypeptide that comprises a cell-specific bindingdomain; and screening the library to identify a experimentally generated(in vitro &/or in vivo) polynucleotide that encodes a binding moleculethat can bind to a nucleic acid and to a cell-specific receptor. Targetcells of particular interest include antigen-presenting andantigen-processing cells, such as muscle cells, monocytes, dendriticcells, B cells, Langerhans cells, keratinocytes, and M-cells.

In some embodiments, the methods of the invention for obtaining acell-specific binding moiety useful for increasing uptake or specificityof a genetic vaccine to a target cell involve:

-   -   (1) reassembling (&/or subjecting to one or more directed        evolution methods described herein) at least first and second        forms of a nucleic acid which comprises a polynucleotide that        encodes a nucleic acid binding domain and at least first and        second forms of a nucleic acid which comprises a cell-specific        ligand that specifically binds to a protein on the surface of a        cell of interest, wherein the first and second forms differ from        each other in two or more nucleotides, to produce a library of        recombinant binding moiety-encoding nucleic acids;    -   (2) transfecting into a population of host cells a library of        vectors, each of which comprises: a) a binding site specific for        the nucleic acid binding domain and b) a member of the library        of recombinant binding moiety-encoding nucleic acids, wherein        the recombinant binding moiety is expressed and binds to the        binding site to form a vector-binding moiety complex;    -   (3) lysing the host cells under conditions that do not disrupt        binding of the vector-binding moiety complex;    -   (4) contacting the vector-binding moiety complex with a target        cell of interest; and    -   (5) identifying target cells that contain a vector and isolating        the optimized recombinant cell-specific binding moiety nucleic        acids from these target cells.

If further optimization is desired, the methods can further involve:

-   -   (6) reassembling (&/or subjecting to one or more directed        evolution methods described herein) at least one optimized        recombinant binding moiety-encoding nucleic acid with a further        form of the polynucleotide that encodes a nucleic acid binding        domain and/or a further form of the polynucleotide that encodes        a cell-specific ligand, which are the same or different from the        first and second forms, to produce a further library of        recombinant binding moiety-encoding nucleic acids;    -   (7) transfecting into a population of host cells a library of        vectors that comprise: a) a binding site specific for the        nucleic acid binding domain and 2) the recombinant binding        moiety-encoding nucleic acids, wherein the recombinant binding        moiety is expressed and binds to the binding site to form a        vector-binding moiety complex;    -   (8) lysing the host cells under conditions that do not disrupt        binding of the vector-binding moiety complex;    -   (9) contacting the vector-binding moiety complex with a target        cell of interest and identifying target cells that contain the        vector; and    -   (10) isolating the optimized recombinant binding moiety nucleic        acids from the target cells which contain the vector; and    -   (11) repeating (6) through (10), as necessary, to obtain a        further optimized cell-specific binding moiety useful for        increasing uptake or specificity of a genetic vaccine vector to        a target cell.

The invention also provides cell-specific recombinant binding moietiesproduced by expressing in a host cell an optimized recombinant bindingmoiety-encoding nucleic acid obtained by the methods of the invention.

In another embodiment, the invention provides genetic vaccines thatinclude: a) an optimized recombinant binding moiety that comprises anucleic acid binding domain and a cell-specific ligand, and b) apolynucleotide sequence that comprises a binding site, wherein thenucleic acid binding domain is capable of specifically binding to thebinding site.

A further embodiment of the invention provides methods for obtaining anoptimized cell-specific binding moiety useful for increasing uptake,efficacy, or specificity of a genetic vaccine for a target cell by:

-   -   (0) reassembling (&/or subjecting to one or more directed        evolution methods described herein) at least first and second        forms of a nucleic acid that comprises a polynucleotide which        encodes a non-toxic receptor binding moiety of an enterotoxin or        other toxin, wherein the first and second forms differ from each        other in two or more nucleotides, to produce a library of        recombinant nucleic acids;    -   (2) transfecting vectors that contain the library of nucleic        acids into a population of host cells, wherein the nucleic acids        are expressed to form recombinant cell-specific binding moiety        polypeptides;    -   (3) contacting the recombinant cell-specific binding moiety        polypeptides with a cell surface receptor of a target cell; and    -   (4) determining which recombinant cell-specific binding moiety        polypeptides exhibit enhanced ability to bind to the target        cell. Methods of enhancing uptake of a genetic vaccine vector by        a target cell by coating the genetic vaccine vector with an        optimized recombinant cell-specific binding moiety produced by        these methods are also provided by the invention.

The present invention also provides methods for evolving a vaccinedelivery vehicle, genetic vaccine vector, or a vector component toobtain an optimized delivery vehicle or component that has, or confersupon a vector, enhanced ability to enter a selected mammalian tissueupon administration to a mammal. These methods involve:

-   -   (1) reassembling (&/or subjecting to one or more directed        evolution methods described herein) members of a pool of        polynucleotides to produce a library of experimentally generated        (in vitro &/or in vivo) polynucleotides;    -   (2) administering to a test animal a library of replicable        genetic packages, each of which comprises a member of the        library of experimentally generated (in vitro &/or in vivo)        polynucleotides operably linked to a polynucleotide that encodes        a display polypeptide, wherein the experimentally generated (in        vitro &/or in vivo) polynucleotide and the display polypeptide        are expressed as a fusion protein which is displayed on the        surface of the replicable genetic package; and    -   (3) recovering replicable genetic packages that are present in        the selected tissue of the test animal at a suitable time after        administration, wherein recovered replicable genetic packages        have enhanced ability to enter the selected mammalian tissue        upon administration to the mammal.

If further optimization of the delivery vehicle is desired, the methodsof the invention further involve:

-   -   (4) reassembling (&/or subjecting to one or more directed        evolution methods described herein) a nucleic acid that        comprises at least one experimentally generated (in vitro &/or        in vivo) polynucleotide obtained from a replicable genetic        package recovered from the selected tissue with a further pool        of polynucleotides to produce a further library of        experimentally generated (in vitro &/or in vivo)        polynucleotides;    -   (5) administering to a test animal a library of replicable        genetic packages, each of which comprises a member of the        further library of experimentally generated (in vitro &/or in        vivo) polynucleotides operably linked to a polynucleotide that        encodes a display polypeptide, wherein the experimentally        generated (in vitro &/or in vivo) polynucleotide and the display        polypeptide are expressed as a fusion protein which is displayed        on the surface of the replicable genetic package;    -   (6) recovering replicable genetic packages that are present in        the selected tissue of the test animal at a suitable time after        administration; and    -   (7) repeating (4) through (6), as necessary, to obtain a further        optimized recombinant delivery vehicle that exhibits further        enhanced ability to enter a selected mammalian tissue upon        administration to a mammal. Methods of administration that are        of particular interest include, for example, oral, topical, and        inhalation. Where the administration is intravenous, mammalian        tissues of interest include, for example, lymph node and spleen.

In another embodiment, the invention provides methods for evolving avaccine delivery vehicle, genetic vaccine vector, or a vector componentto obtain an optimized delivery vehicle or component to obtain anoptimized delivery vehicle or vector component that has, or confers upona vector containing the component, enhanced specificity forantigen-presenting cells by:

-   -   (0) reassembling (&/or subjecting to one or more directed        evolution methods described herein) members of a pool of        polynucleotides to produce a library of experimentally generated        (in vitro &/or in vivo) polynucleotides;    -   (1) producing a library of replicable genetic packages, each of        which comprises a member of the library of experimentally        generated (in vitro &/or in vivo) polynucleotides operably        linked to a polynucleotide that encodes a display polypeptide,        wherein the experimentally generated (in vitro &/or in vivo)        polynucleotide and the display polypeptide are expressed as a        fusion protein which is displayed on the surface of the        replicable genetic package;    -   (3) contacting the library of recombinant replicable genetic        packages with a non-APC to remove replicable genetic packages        that display non-APC-specific fusion polypeptides; and    -   (4) contacting the recombinant replicable genetic packages that        did not bind to the non-APC with an APC and recovering those        that bind to the APC, wherein the recovered replicable genetic        packages are capable of specifically binding to APCs.

In an additional embodiment, the invention provides methods for evolvinga vaccine delivery vehicle, genetic vaccine vector, or a vectorcomponent to obtain an optimized delivery vehicle or component to obtainan optimized delivery vehicle or vector component that has, or confersupon a vector containing the component, an enhanced ability to enter atarget cell by:

-   -   (0) reassembling (&/or subjecting to one or more directed        evolution methods described herein) at least first and second        forms of a nucleic acid which encodes an invasin polypeptide,        wherein the first and second forms differ from each other in two        or more nucleotides, to produce a library of recombinant invasin        nucleic acids;    -   (2) producing a library of recombinant bacteriophage, each of        which displays on the bacteriophage surface a fusion polypeptide        encoded by a chimeric gene that comprises a recombinant invasin        nucleic acid operably linked to a polynucleotide that encodes a        display polypeptide;    -   (3) contacting the library of recombinant bacteriophage with a        population of target cells;    -   (4) removing unbound phage and phage which is bound to the        surface of the target cells; and    -   (5) recovering phage which are present within the target cells,        wherein the recovered phage are enriched for phage that have        enhanced ability to enter the target cells.

In some embodiments, the optimized recombinant genetic vaccine vectors,delivery vehicles, or vector components obtained using these methodsexhibit improved ability to enter an antigen presenting cell. Thesemethods can involve washing the cells after the transfection step toremove vectors which did not enter an antigen presenting cell; culturingthe cells for a predetermined time after transfection; lysing theantigen presenting cells; and isolating the optimized recombinantgenetic vaccine vector from the cell lysate.

Antigen Presenting Cells that Contain an Optimized Recombinant GeneticVaccine Vectors can be Identified by, for Example, Detecting Expressionof a Marker Gene that is Included in the Vectors.

The invention also provides methods of evolving a bacteriophage-derivedvaccine delivery vehicle to obtain a delivery vehicle having enhancedability to enter a target cell. These methods involve the steps of:

-   -   (1) reassembling (&/or subjecting to one or more directed        evolution methods described herein) at least first and second        forms of a nucleic acid which encodes an invasin polypeptide,        wherein the first and second forms differ from each other in two        or more nucleotides, to produce a library of recombinant invasin        nucleic acids;    -   (2) producing a library of recombinant bacteriophage, each of        which displays on the bacteriophage surface a fusion polypeptide        encoded by a chimeric gene that comprises a recombinant invasin        nucleic acid operably linked to a polynucleotide that encodes a        display polypeptide;    -   (3) contacting the library of recombinant bacteriophage with a        population of target cells;    -   (4) removing unbound phage and phage which is bound to the        surface of the target cells; and    -   (5) recovering phage which are present within the target cells,        wherein the recovered phage are enriched for phage that have        enhanced ability to enter the target cells. Again, if further        optimization is desired, the methods can include the further        steps of:    -   (6) reassembling (&/or subjecting to one or more directed        evolution methods described herein) a nucleic acid which        comprises at least one recombinant invasin nucleic acid obtained        from a bacteriophage which is recovered from a target cell with        a further pool of polynucleotides to produce a further library        of recombinant invasin polynucleotides;    -   (7) producing a further library of recombinant bacteriophage,        each of which displays on the bacteriophage surface a fusion        polypeptide encoded by a chimeric gene that comprises a        recombinant invasin nucleic acid operably linked to a        polynucleotide that encodes a display polypeptide;    -   (8) contacting the library of recombinant bacteriophage with a        population of target cells;    -   (9) removing unbound phage and phage which is bound to the        surface of the target cells; and    -   (10) recovering phage which are present within the target cells;        and    -   (11) repeating (6) through (10), as necessary, to obtain a        further optimized recombinant delivery vehicle which exhibits        further have enhanced ability to enter the target cells.

In some embodiments the methods of evolving a bacteriophage-derivedvaccine delivery vehicle to obtain a delivery vehicle having enhancedability to enter a target cell can include the additional steps of:

-   -   (12) inserting into the optimized recombinant delivery vehicle a        polynucleotide which encodes an antigen of interest, wherein the        antigen of interest is expressed as a fusion polypeptide which        comprises a second display polypeptide;    -   (13) administering the delivery vehicle to a test animal;        and (14) determining whether the delivery vehicle is capable of        inducing a CTL response in the test animal.

Alternatively, the following steps can be employed:

-   -   (12) inserting into the optimized recombinant delivery vehicle a        polynucleotide which encodes an antigen of interest, wherein the        antigen of interest is expressed as a fusion polypeptide which        comprises a second display polypeptide;    -   (13) administering the delivery vehicle to a test animal; and    -   (14) determining whether the delivery vehicle is capable of        inducing neutralizing antibodies against a pathogen which        comprises the antigen of interest. An example of a target cell        of interest for these methods is an antigen-presenting cell.

The present invention provides recombinant multivalent antigenicpolypeptides that include a first antigenic determinant from a firstdisease-associated polypeptide and at least a second antigenicdeterminant from a second disease-associated polypeptide. Thedisease-associated polypeptides can be selected from the groupconsisting of cancer antigens, antigens associated with autoimmunitydisorders, antigens associated with inflammatory conditions, antigensassociated with allergic reactions, antigens associated with infectiousagents, and other antigens that are associated with a disease condition.

In another embodiment, the invention provides a recombinant antigenlibrary that contains recombinant nucleic acids that encode antigenicpolypeptides. The libraries are typically obtained by reassembling (&/orsubjecting to one or more directed evolution methods described herein),at least first and second forms of a nucleic acid which includes apolynucleotide sequence that encodes a disease-associated antigenicpolypeptide, wherein the first and second forms differ from each otherin two or more nucleotides, to produce a library of recombinant nucleicacids.

Another embodiment of the invention provides methods of obtaining apolynucleotide that encodes a recombinant antigen having improvedability to induce an immune response to a disease condition. Thesemethods involve:

-   -   (1) reassembling (&/or subjecting to one or more directed        evolution methods described herein) at least first and second        forms of a nucleic acid which comprises a polynucleotide        sequence that encodes an antigenic polypeptide that is        associated with the disease condition, wherein the first and        second forms differ from each other in two or more nucleotides,        to produce a library of recombinant nucleic acids; and    -   (1) screening the library to identify at least one optimized        recombinant nucleic acid that encodes an optimized recombinant        antigenic polypeptide that has improved ability to induce an        immune response to the disease condition.        These methods optionally further involve:    -   (3) reassembling (&/or subjecting to one or more directed        evolution methods described herein) at least one optimized        recombinant nucleic acid with a further form of the nucleic        acid, which is the same or different from the first and second        forms, to produce a further library of recombinant nucleic        acids;    -   (4) screening the further library to identify at least one        further optimized recombinant nucleic acid that encodes a        polypeptide that has improved ability to induce an immune        response to the disease condition; and    -   (5) repeating (3) and (4), as necessary, until the further        optimized recombinant nucleic acid encodes a polypeptide that        has improved ability to induce an immune response to the disease        condition.

In some embodiments, the optimized recombinant nucleic acid encodes amultivalent antigenic polypeptide and the screening is accomplished byexpressing the library of recombinant nucleic acids in a phage displayexpression vector such that the recombinant antigen is expressed as afusion protein with a phage polypeptide that is displayed on a phageparticle surface; contacting the phage with a first antibody that isspecific for a first serotype of the pathogenic agent and selectingthose phage that bind to the first antibody; and contacting those phagethat bind to the first antibody with a second antibody that is specificfor a second serotype of the pathogenic agent and selecting those phagethat bind to the second antibody; wherein those phage that bind to thefirst antibody and the second antibody express a multivalent antigenicpolypeptide.

The Invention Also Provides Methods of Obtaining a Recombinant ViralVector which has an Enhanced Ability to Induce an Antiviral Response ina Cell.

Methods of Obtaining a Recombinant Genetic Vaccine Component thatConfers Upon a Genetic Vaccine an Enhanced Ability to Induce a DesiredImmune Response in a Mammal

In additional embodiments, the invention provides methods of obtaining arecombinant genetic vaccine component that confers upon a geneticvaccine an enhanced ability to induce a desired immune response in amammal. These methods involve: (1) reassembling (&/or subjecting to oneor more directed evolution methods described herein) at least first andsecond forms of a nucleic acid which comprise a genetic vaccine vector,wherein the first and second forms differ from each other in two or morenucleotides, to produce a library of recombinant genetic vaccinevectors; (2) transfecting the library of recombinant vaccine vectorsinto a population of mammalian cells selected from the group consistingof peripheral blood T cells, T cell clones, freshly isolatedmonocytes/macrophages and dendritic cells; (3) staining the cells forthe presence of one or more cytokines and identifying cells whichexhibit a cytokine staining pattern indicative of the desired immuneresponse; and (4) obtaining recombinant vaccine vector nucleic acidsequences from the cells which exhibit the desired cytokine stainingpattern.

Methods of Improving the Ability of a Genetic Vaccine Vector to Modulatean Immune Response.

Also provided by the invention are methods of improving the ability of agenetic vaccine vector to modulate an immune response by: (1)reassembling (&/or subjecting to one or more directed evolution methodsdescribed herein) at least first and second forms of a nucleic acidwhich comprise a genetic vaccine vector, wherein the first and secondforms differ from each other in two or more nucleotides, to produce alibrary of recombinant genetic vaccine vectors; (2) transfecting thelibrary of recombinant genetic vaccine vectors into a population ofantigen presenting cells; and (3) isolating from the cells optimizedrecombinant genetic vaccine vectors which exhibit enhanced ability tomodulate a desired immune response.

Methods of Obtaining a Recombinant Genetic Vaccine Vector that has anEnhanced Ability to Induce a Desired Immune Response in a Mammal UponAdministration to the Skin of the Mammal.

Another embodiment of the invention provides methods of obtaining arecombinant genetic vaccine vector that has an enhanced ability toinduce a desired immune response in a mammal upon administration to theskin of the mammal. These methods involve: (1) reassembling (&/orsubjecting to one or more directed evolution methods described herein)at least first and second forms of a nucleic acid which comprise agenetic vaccine vector, wherein the first and second forms differ fromeach other in two or more nucleotides, to produce a library ofrecombinant genetic vaccine vectors; (2) topically applying the libraryof recombinant genetic vaccine vectors to skin of a mammal; (3)identifying vectors that induce an immune response; and (4) recoveringgenetic vaccine vectors from the skin cells which contain vectors thatinduce an immune response.

Methods of Inducing an Immune Response in a Mammal by Topically Applyingto Skin of the Mammal a Genetic Vaccine Vector, Wherein the GeneticVaccine Vector is Optimized for Topical Application Through Use ofStochastic (e.g. Polynucleotide Shuffling & Interrupted Synthesis) andNon-Stochastic Polynucleotide Reassembly

The invention also provides methods of inducing an immune response in amammal by topically applying to skin of the mammal a genetic vaccinevector, wherein the genetic vaccine vector is optimized for topicalapplication through use of stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassembly. Insome embodiments, the genetic vaccine is administered as a formulationselected from the group consisting of a transdermal patch, a cream,naked DNA, a mixture of DNA and a transfection-enhancing agent. Suitabletransfection-enhancing agents include one or more agents selected fromthe group consisting of a lipid, a liposome, a protease, and a lipase.

Alternatively, or in addition, the genetic vaccine can be administeredafter pretreatment of the skin by abrasion or hair removal.

Methods of Obtaining an Optimized Genetic Vaccine Component that ConfersUpon a Genetic Vaccine Containing the Component an Enhanced Ability toInduce or Inhibit Apoptosis of a Cell into which the Vaccine isIntroduced.

In another embodiment, the invention provides methods of obtaining anoptimized genetic vaccine component that confers upon a genetic vaccinecontaining the component an enhanced ability to induce or inhibitapoptosis of a cell into which the vaccine is introduced. These methodsinvolve: (1) reassembling (&/or subjecting to one or more directedevolution methods described herein) at least first and second forms of anucleic acid which comprise a nucleic acid that encodes anapoptosis-modulating polypeptide, wherein the first and second formsdiffer from each other in two or more nucleotides, to produce a libraryof recombinant nucleic acids; (2) transfecting the library ofrecombinant nucleic acids into a population of mammalian cells; (3)staining the cells for the presence of a cell membrane change which isindicative of apoptosis initiation; and (4) obtaining recombinantapoptosis-modulating genetic vaccine components from the cells whichexhibit the desired apoptotic membrane changes.

Methods of Obtaining a Genetic Vaccine Component that Confers Upon aGenetic Vaccine Reduced Susceptibility to a CTL Immune Response in aHost Mammal.

Other embodiments of the invention provide methods of obtaining agenetic vaccine component that confers upon a genetic vaccine reducedsusceptibility to a CTL immune response in a host mammal. These methodscan involve: (1) reassembling (&/or subjecting to one or more directedevolution methods described herein) at least first and second forms of anucleic acid which comprises a gene that encodes an inhibitor of a CTLimmune response, wherein the first and second forms differ from eachother in two or more nucleotides, to produce a library of recombinantCTL inhibitor nucleic acids; (2) introducing genetic vaccine vectorswhich comprise the library of recombinant CTL inhibitor nucleic acidsinto a plurality of human cells; (3) selecting cells which exhibitreduced MHC class I molecule expression; and (4) obtaining optimizedrecombinant CTL inhibitor nucleic acids from the selected cells.

Methods of Obtaining a Genetic Vaccine Component that Confers Upon aGenetic Vaccine Reduced Susceptibility to a CTL Immune Response in aHost Mammal.

The invention also provides methods of obtaining a genetic vaccinecomponent that confers upon a genetic vaccine reduced susceptibility toa CTL immune response in a host mammal. These methods involve: (1)reassembling (&/or subjecting to one or more directed evolution methodsdescribed herein) at least first and second forms of a nucleic acidwhich comprises a gene that encodes an inhibitor of a CTL immuneresponse, wherein the first and second forms differ from each other intwo or more nucleotides, to produce a library of recombinant CTLinhibitor nucleic acids; (2) introducing viral vectors which comprisethe library of recombinant CTL inhibitor nucleic acids into mammaliancells; (3) identifying mammalian cells which express a marker geneincluded in the viral vectors a predetermined time after introduction,wherein the identified cells are resistant to a CTL response; and (4)recovering as the genetic vaccine component the recombinant CTLinhibitor nucleic acids from the identified cells.

It is a general object of the invention to provide proteins andpolypeptides that are derived from PfEMP1 proteins, nucleic acidsencoding these proteins and antibodies that are specificallyimmunoreactive with these proteins. It is a further object to providemethods of using these various compositions in diagnosis, treatment orprevention of the onset of symptoms of a malaria parasite infection. Itis a further object to provide methods of screening compounds toidentify further compositions which may be used in these methods.

In one embodiment, the present invention provides substantially purepolypeptides which have amino acid sequences substantially homologous tothe amino acid sequence of a PfEMP1 protein, or biologically activefragments thereof.

In preferred aspects, the polypeptides of the present invention aresubstantially homologous to the amino acid sequence shown, described&/or referenced herein (including incorporated by reference),biologically active fragments or analogues thereof. Also provided arepharmaceutical compositions comprising these polypeptides.

In another embodiment, the present invention provides nucleic acidswhich encode the above-described polypeptides. Particularly preferrednucleic acids will be substantially homologous to a part or whole of thenucleic acid sequence shown, described &/or referenced herein (includingincorporated by reference) or the nucleic acid encoding for thesequences shown, described &/or referenced herein (includingincorporated by reference). The present invention also providesexpression vectors comprising these nucleic acid sequences and cellscapable of expressing same.

In an additional embodiment, the present invention provides antibodieswhich recognize and bind PfEMP1 polypeptides or biologically activefragments thereof. More preferred are those peptides which recognize andbind PfEMP1 proteins associated with infection by more than one variantof P. falciparum.

In a further embodiment, the present invention provides methods ofinhibiting the formation of PfEMP1/ligand complex, comprising contactingPfEMP1 or its ligands with polypeptides of the present invention.

In a related embodiment, the present invention provides methods ofinhibiting sequestration of erythrocytes in a patient suffering from amalaria infection, comprising administering to said patient, aneffective amount of a polypeptide of the present invention. Suchadministration may be carried out prior to or following infection.

In still another embodiment, the present invention provides a method ofdetecting the presence or absence of PfEMP1 in a sample. The methodcomprises exposing the sample to an antibody of the invention, anddetecting binding, if any, between the antibody and a component of thesample.

In an additional embodiment, the present invention provides a method ofdetermining whether a test compound is an antagonist of PfEMP1/ligandcomplex formation. The method comprises incubating the test compoundwith PfEMP1 or a biologically active fragment thereof, and its ligand,under conditions which permit the formation of the complex. The amountof complex formed in the presence of the test compound is determined andcompared with the amount of complex formed in the absence of the testcompound. A decrease in the amount of complex formed in the presence ofthe test compound is indicative that the compound is an antagonist ofPfEMP1/ligand complex formation.

Summary of Directed Evolution Approaches

This invention also relates generally to the field of nucleic acidengineering and correspondingly encoded recombinant protein engineering.More particularly, the invention relates to the directed evolution ofnucleic acids and screening of clones containing the evolved nucleicacids for resultant activity(ies) of interest, such nucleic acidactivity(ies) &/or specified protein, particularly enzyme, activity(ies)of interest.

Mutagenized molecules provided by this invention may have chimericmolecules and molecules with point mutations, including biologicalmolecules that contain a carbohydrate, a lipid, a nucleic acid, &/or aprotein component, and specific but non-limiting examples of theseinclude antibiotics, antibodies, enzymes, and steroidal andnon-steroidal hormones.

This invention relates generally to a method of: 1) preparing a progenygeneration of molecule(s) (including a molecule that is comprised of apolynucleotide sequence, a molecule that is comprised of a polypeptidesequence, and a molecule that is comprised in part of a polynucleotidesequence and in part of a polypeptide sequence), that is mutagenized toachieve at least one point mutation, addition, deletion, &/orchimerization, from one or more ancestral or parental generationtemplate(s); 2) screening the progeny generation molecule(s)—preferablyusing a high throughput method—for at least one property of interest(such as an improvement in an enzyme activity or an increase instability or a novel chemotherapeutic effect); 3) optionally obtaining&/or cataloguing structural &/or and functional information regardingthe parental &/or progeny generation molecules; and 4) optionallyrepeating any of steps 1) to 3).

In a preferred embodiment, there is generated (e.g. from a parentpolynucleotide template)—in what is termed “codon site-saturationmutagenesis”—a progeny generation of polynucleotides, each having atleast one set of up to three contiguous point mutations (i.e. differentbases comprising a new codon), such that every codon (or every family ofdegenerate codons encoding the same amino acid) is represented at eachcodon position. Corresponding to—and encoded by—this progeny generationof polynucleotides, there is also generated a set of progenypolypeptides, each having at least one single amino acid point mutation.In a preferred aspect, there is generated—in what is termed “amino acidsite-saturation mutagenesis”—one such mutant polypeptide for each of the19 naturally encoded polypeptide-forming alpha-amino acid substitutionsat each and every amino acid position along the polypeptide. Thisyields—for each and every amino acid position along the parentalpolypeptide—a total of 20 distinct progeny polypeptides including theoriginal amino acid, or potentially more than 21 distinct progenypolypeptides if additional amino acids are used either instead of or inaddition to the 20 naturally encoded amino acids

Thus, in another aspect, this approach is also serviceable forgenerating mutants containing—in addition to &/or in combination withthe 20 naturally encoded polypeptide-forming alpha-amino acids—otherrare &/or not naturally-encoded amino acids and amino acid derivatives.In yet another aspect, this approach is also serviceable for generatingmutants by the use of—in addition to &/or in combination with natural orunaltered codon recognition systems of suitable hosts—altered,mutagenized, &/or designer codon recognition systems (such as in a hostcell with one or more altered tRNA molecules).

In yet another aspect, this invention relates to recombination and morespecifically to a method for preparing polynucleotides encoding apolypeptide by a method of in vivo re-assortment of polynucleotidesequences containing regions of partial homology, assembling thepolynucleotides to form at least one polynucleotide and screening thepolynucleotides for the production of polypeptide(s) having a usefulproperty.

In yet another preferred embodiment, this invention is serviceable foranalyzing and cataloguing—with respect to any molecular property (e.g.an enzymatic activity) or combination of properties allowed by currenttechnology—the effects of any mutational change achieved (includingparticularly saturation mutagenesis). Thus, a comprehensive method isprovided for determining the effect of changing each amino acid in aparental polypeptide into each of at least 19 possible substitutions.This allows each amino acid in a parental polypeptide to becharacterized and catalogued according to its spectrum of potentialeffects on a measurable property of the polypeptide.

In another aspect, the method of the present invention utilizes thenatural property of cells to recombine molecules and/or to mediatereductive processes that reduce the complexity of sequences and extentof repeated or consecutive sequences possessing regions of homology.

It is an object of the present invention to provide a method forgenerating hybrid polynucleotides encoding biologically active hybridpolypeptides with enhanced activities. In accomplishing these and otherobjects, there has been provided, in accordance with one aspect of theinvention, a method for introducing polynucleotides into a suitable hostcell and growing the host cell under conditions that produce a hybridpolynucleotide.

In another aspect of the invention, the invention provides a method forscreening for biologically active hybrid polypeptides encoded by hybridpolynucleotides. The present method allows for the identification ofbiologically active hybrid polypeptides with enhanced biologicalactivities.

1.4. Brief Description of the Drawings

FIG. 1. Exonuclease Activity. FIG. 1 shows the activity of the enzymeexonuclease m. This is an exemplary enzyme that can be used to shuffle,assemble, reassemble, recombine, and/or concatenate polynucleotidebuilding blocks. The asterisk indicates that the enzyme acts from the 3′direction towards the 5′ direction of the polynucleotide substrate.

FIG. 2. Generation of A Nucleic Acid Building Block by Polymerase-BasedAmplification. FIG. 2 illustrates a method of generating adouble-stranded nucleic acid building block with two overhangs using apolymerase-based amplification reaction (e.g., PCR). As illustrated, afirst polymerase-based amplification reaction using a first set ofprimers, F₂ and R1, is used to generate a blunt-ended product (labeledReaction 1, Product 1), which is essentially identical to Product A. Asecond polymerase-based amplification reaction using a second set ofprimers, F₁ and R₂, is used to generate a blunt-ended product (labeledReaction 2, Product 2), which is essentially identical to Product B.These two products are then mixed and allowed to melt and anneal,generating a potentially useful double-stranded nucleic acid buildingblock with two overhangs. In the example of FIG. 1, the product with the3′ overhangs (Product C) is selected for by nuclease-based degradationof the other 3 products using a 3′ acting exonuclease, such asexonuclease III. Alternate primers are shown in parenthesis toillustrate serviceable primers may overlap, and additionally thatserviceable primers may be of different lengths, as shown.

FIG. 3. Unique Overhangs And Unique Couplings. FIG. 3 illustrates thepoint that the number of unique overhangs of each size (e.g. the totalnumber of unique overhangs composed of 1 or 2 or 3, etc. nucleotides)exceeds the number of unique couplings that can result from the use ofall the unique overhangs of that size. For example, there are 4 unique3′ overhangs composed of a single nucleotide, and 4 unique 5′ overhangscomposed of a single nucleotide. Yet the total number of uniquecouplings that can be made using all the 8 unique single-nucleotide 3′overhangs and single-nucleotide 5′ overhangs is 4.

FIG. 4. Unique Overall Assembly Order Achieved by Sequentially Couplingthe Building Blocks

FIG. 4 illustrates the fact that in order to assemble a total of “n”nucleic acid building blocks, “n−1” couplings are needed. Yet it issometimes the case that the number of unique couplings available for useis fewer that the “n−1” value. Under these, and other, circumstances astringent non-stochastic overall assembly order can still be achieved byperforming the assembly process in sequential steps. In this example, 2sequential steps are used to achieve a designed overall assembly orderfor five nucleic acid building blocks. In this illustration the designedoverall assembly order for the five nucleic acid building blocks is:5′-(#1-#2-#3-#4-#5)-3′, where #1 represents building block number 1,etc.

FIG. 5. Unique Couplings Available Using a Two-Nucleotide 3′ Overhang.FIG. 5 further illustrates the point that the number of unique overhangsof each size (here, e.g. the total number of unique overhangs composedof 2 nucleotides) exceeds the number of unique couplings that can resultfrom the use of all the unique overhangs of that size. For example,there are 16 unique 3′ overhangs composed of two nucleotides, andanother 16 unique 5′ overhangs composed of two nucleotides, for a totalof 32 as shown. Yet the total number of couplings that are unique andnot self-binding that can be made using all the 32 uniquedouble-nucleotide 3′ overhangs and double-nucleotide 5′ overhangs is 12.Some apparently unique couplings have “identical twins” (marked in thesame shading), which are visually obvious in this illustration. Stillother overhangs contain nucleotide sequences that can self-bind in apalindromic fashion, as shown and labeled in this figure; thus they notcontribute the high stringency to the overall assembly order.

FIG. 6. Generation of an Exhaustive Set of Chimeric Combinations bySynthetic Ligation Reassembly. FIG. 6 showcases the power of thisinvention in its ability to generate exhaustively and systematically allpossible combinations of the nucleic acid building blocks designed inthis example. Particularly large sets (or libraries) of progeny chimericmolecules can be generated. Because this method can be performedexhaustively and systematically, the method application can be repeatedby choosing new demarcation points and with correspondingly newlydesigned nucleic acid building blocks, bypassing the burden ofre-generating and re-screening previously examined and rejectedmolecular species. It is appreciated that, codon wobble can be used toadvantage to increase the frequency of a demarcation point. In otherwords, a particular base can often be substituted into a nucleic acidbuilding block without altering the amino acid encoded by progenitorcodon (that is now altered codon) because of codon degeneracy. Asillustrated, demarcation points are chosen upon alignment of 8progenitor templates. Nucleic acid building blocks including theiroverhangs (which are serviceable for the formation of ordered couplings)are then designed and synthesized. In this instance, 18 nucleic acidbuilding blocks are generated based on the sequence of each of the 8progenitor templates, for a total of 144 nucleic acid building blocks(or double-stranded oligos). Performing the ligation synthesis procedurewill then produce a library of progeny molecules comprised of yield of8¹⁸ (or over 1.8×10¹⁶) chimeras.

FIG. 7. Synthetic genes from oligos. According to one embodiment of thisinvention, double-stranded nucleic acid building blocks are designed byaligning a plurality of progenitor nucleic acid templates. Preferablythese templates contain some homology and some heterology. The nucleicacids may encode related proteins, such as related enzymes, whichrelationship may be based on function or structure or both. FIG. 7 showsthe alignment of three polynucleotide progenitor templates and theselection of demarcation points (boxed) shared by all the progenitormolecules. In this particular example, the nucleic acid building blocksderived from each of the progenitor templates were chosen to beapproximately 30 to 50 nucleotides in length.

FIG. 8. Nucleic acid building blocks for synthetic ligation genereassembly. FIG. 8 shows the nucleic acid building blocks from theexample in FIG. 7. The nucleic acid building blocks are shown here ingeneric cartoon form, with their compatible overhangs, including both 5′and 3′ overhangs. There are 22 total nucleic acid building blocksderived from each of the 3 progenitor templates. Thus, the ligationsynthesis procedure can produce a library of progeny molecules comprisedof yield of 3²² (or over 3.1×10¹⁰) chimeras.

FIG. 9. Addition of Introns by Synthetic Ligation Reassembly. FIG. 9shows in generic cartoon form that an intron may be introduced into achimeric progeny molecule by way of a nucleic acid building block. It isappreciated that introns often have consensus sequences at both terminiin order to render them operational. It is also appreciated that, inaddition to enabling gene splicing, introns may serve an additionalpurpose by providing sites of homology to other nucleic acids to enablehomologous recombination. For this purpose, and potentially others, itmay be sometimes desirable to generate a large nucleic acid buildingblock for introducing an intron. If the size is overly large easilygenerating by direct chemical synthesis of two single stranded oligos,such a specialized nucleic acid building block may also be generated bydirect chemical synthesis of more than two single stranded oligos or byusing a polymerase-based amplification reaction as shown, described &/orreferenced herein (including incorporated by reference).

FIG. 10. Ligation Reassembly Using Fewer Than All The Nucleotides Of AnOverhang. FIG. 10 shows that coupling can occur in a manner that doesnot make use of every nucleotide in a participating overhang. Thecoupling is particularly lively to survive (e.g. in a transformed host)if the coupling reinforced by treatment with a ligase enzyme to formwhat may be referred to as a “gap ligation” or a “gapped ligation”. Itis appreciated that, as shown, this type of coupling can contribute togeneration of unwanted background product(s), but it can also be usedadvantageously increase the diversity of the progeny library generatedby the designed ligation reassembly.

FIG. 11. Avoidance of unwanted self-ligation in palindromic couplings.As mentioned before and shown, described &/or referenced herein(including incorporated by reference), certain overhangs are able toundergo self-coupling to form a palindromic coupling. A coupling isstrengthened substantially if it is reinforced by treatment with aligase enzyme. Accordingly, it is appreciated that the lack of 5′phosphates on these overhangs, as shown, can be used advantageously toprevent this type of palindromic self-ligation. Accordingly, thisinvention provides that nucleic acid building blocks can be chemicallymade (or ordered) that lack a 5′ phosphate group (or alternatively theycan be removed—e.g. by treatment with a phosphatase enzyme such as acalf intestinal alkaline phosphatase (CIAP)—in order to preventpalindromic self-ligations in ligation reassembly processes.

FIG. 12. Site-directed mutagenesis by polymerase-based extension. PanelA. This figure shows one method of site-directed mutagenesis, among manymethods of site-directed mutagenesis, that are serviceable forperforming site-saturation mutagenesis. Section (1) shows the first andsecond mutagenic primer annealed to a circular closed double-strandedplasmid. The dot and the open-sided triangle indicate the mutagenicsites in the mutagenic primers. The arrows indicate the direction ofsynthesis. Section (2) shows the newly synthesized (mutagenized) DNAstrands annealed to each other. The parental DNA can be treated with aselection enzyme. The mutagenized DNA strands are shown as beingannealed to form a double-stranded mutagenized circular DNAintermediate. The dot and the open-sided triangle indicate the mutagenicsites in the experimentally generated progeny (mutagenized) DNA strands.Note that the staggered openings on the mutagenized DNA strands form“sticky” ends. Section (3) shows the first and second mutagenic primerannealed to the mutagenized DNA strands of Section (2). The arrowsindicate the direction of synthesis. Note the opening on each of themutagenized DNA strands (i.e. they have not been ligated). Section (4)shows a “Gapped Product”, which is composed of second generationmutagenized DNA strands, synthesized using the mutagenized DNA strands(shown in Step (2)) as a template. The DNA strands of the “GappedProduct” are shown as being annealed to form a double-strandedmutagenized circular DNA intermediate. The dot and the open-sidedtriangle indicate the mutagenic sites in the mutagenized DNA strands.Note the large gap in each of the mutagenized DNA strands. Section (5)shows the “Gapped Product” annealed to the parental (non-mutated)plasmid, enabling polymerase-based synthesis to occur. The arrowsindicate the direction of synthesis. Section (6) shows the newlysynthesized DNA strands, as being annealed to form a double-strandedmutagenized circular DNA product. The dot and the open-sided triangleindicate the mutagenic sites in the mutagenized DNA strands. Note thestaggered openings on the mutagenized DNA strands. Also note thepresence of both mutagenic sites on each of the mutagenized DNA strands.

Panel B. This figure shows two possible molecular structures producedfrom the amplification steps of FIG. 12A. Molecule (A) is shown also inSection (2) of FIG. 12A. Molecule (B) is also shown in Section (6) ofFIG. 12A.

FIG. 13. Site-directed mutagenesis by polymerase-based extension andligase-based ligation. Panel A. This figure shows one method ofsite-directed mutagenesis, among many methods of site-directedmutagenesis, that are serviceable for performing site-saturationmutagenesis. Section (1) shows the first and second mutagenic primerannealed to a circular closed double-stranded plasmid. The dot and theopen-sided triangle indicate the mutagenic sites in the mutagenicprimers. The arrows indicate the direction of synthesis. Section (2)shows the newly synthesized (mutagenized) DNA strands annealed to eachother. The parental DNA can be treated with a selection enzyme. Themutagenized DNA strands are shown as being annealed to form adouble-stranded mutagenized circular DNA intermediate. The dot and theopen-sided triangle indicate the mutagenic sites in the experimentallygenerated progeny (mutagenized) DNA strands. Note that the staggeredopenings on the mutagenized DNA strands form “sticky” ends. Section (3)shows the resultant double-stranded mutagenized circular DNA moleculeproduced after the double-stranded mutagenized circular DNA intermediateof Section (2) is ligated (e.g. with T4 DNA ligase). Section (4) showsthe first and second mutagenic primer annealed to the mutagenized DNAstrands of Section (3). The arrows indicate the direction of synthesis.Section (5) shows the recently generated (blue) mutagenized DNA strandsas being annealed to form a double-stranded mutagenized circular DNAintermediate. The dot and the open-sided triangle indicate the mutagenicsites in the recently generated mutagenized DNA strands (blue). Notethat the staggered openings on the mutagenized DNA strands form “stickyends”. Also note the presence of both mutagenic sites on each of the tworecently generated mutagenized DNA strands (blue). Note the opening oneach of the mutagenized DNA strands (i.e. they have not been ligated).Section (6) shows the resultant double-stranded mutagenized circular DNAmolecule produced after the double-stranded mutagenized circular DNAintermediate of Section (5) is ligated (e.g. using T4 DNA ligase). Thedot and the open-sided triangle indicate the mutagenic sites in themutagenized DNA molecules. Again, note the presence of both mutagenicsites on each of the mutagenized DNA strands.

Panel B. This figure shows two molecular structures produced from theamplification steps of FIG. 13A. Molecule (A) is also shown in Section(3) of FIG. 13A. Molecule (B) is produced in Section (6) of FIG. 13A.

FIG. 14: Strategy for Obtaining and Using Nucleic Acid Binding Proteinsthat Facilitate Entry of Genetic Vaccines.

Shown here is a strategy for obtaining and using nucleic acid bindingproteins that facilitate entry of genetic vaccines, in particular, nakedDNA, into target cells. Members of a library obtained by the directedevolution methods described herein are linked to a coding region of M13protein VIII so that a fusion protein is displayed on the surface of thephage particles. Phage that efficiently enter the desired target tissueare identified, and the fusion protein is then used to coat a geneticvaccine nucleic acid.

FIG. 15: A schematic representation of a method for generating achimeric, multivalent antigen that has immunogenic regions from multipleantigens. Antibodies to each of the non-chimeric parental immunogenicpolypeptides are specific for the respective organisms (A, B, C). Aftercarrying out the directed evolution and selection methods of theinvention, however, a chimeric immunogenic polypeptide is obtained thatis recognized by antibodies raised against each of the three parentalimmunogenic polypeptides.

FIG. 16A and FIG. 16B: Method for Obtaining Non-Stochastically GeneratedPolypeptides that can induce a Broad-Spectrum Immune Response.

Shown here is a schematic for a method by which one can obtainnon-stochastically generated polypeptides that can induce abroad-spectrum immune response. In FIG. 16A, wild-type immunogenicpolypeptides from the pathogens A, B, and C provide protection againstthe corresponding pathogen from which the polypeptide is derived, butlittle or no cross-protection against the other pathogens (left panel).After evolving, an A/B/C chimeric polypeptide is obtained that caninduce a protective immune response against all three pathogen types(right panel). In FIG. 16B, directed evolution is used with substratenucleic acids from two pathogen strains (A, B), which encodepolypeptides that are protective only against the correspondingpathogen. After directed evolution, the resulting chimeric polypeptidecan induce an immune response that is effective against not only the twoparental pathogen strains, but also against a third strain of pathogen(C).

FIG. 17: Possible factors for determining whether a particularpolynucleotide encodes an immunogenic polypeptide having a desiredproperty.

Shown here are some of the possible factors that can determine whether aparticular polynucleotide encodes an immunogenic polypeptide having adesired property, such as enhanced immunogenicity and/orcross-reactivity. Those sequence regions that positively affect aparticular property are indicated as plus signs along the antigen gene,while those sequence regions that have a negative effect are shown asminus signs. A pool of related antigen genes are non-stochasticallygenerated using the methods described herein and screened to obtainthose evolved nucleic acids that have gained positive sequence regionsand lost negative regions. No pre-existing knowledge as to which regionsare positive or negative for a particular trait is required.

FIG. 18: Screening strategy for antigen library screening.

Shown here is a schematic representation of the screening strategy forantigen library screening.

FIG. 19: Strategy for pooling and deconvolution as used in antigenlibrary screening.

Shown here is a schematic representation of a strategy for pooling anddeconvolution as used in antigen library screening.

FIG. 20: Preferred Embodiments of Site-Saturation Mutagenesis.

FIG. 21. Schematic representation of a multimodule genetic vaccinevector. Shown here is a schematic representation of a multimodulegenetic vaccine vector. A typical genetic vaccine vector will includeone or more of the components indicated, each of which can be native oroptimized using the directed evolution methods described herein. Thesedirected evolution methods can include the introduction of pointmutations by stochastic methods &/or by non-stochastic methods,including “gene site saturation mutagenesis” as described herein. Thesedirected evolution methods can also include stochastic polynucleotidereassembly methods, for example by interrupted synthesis (as describedin U.S. Pat. No. 5,965,408). These directed evolution methods can alsoinclude non-stochastic polynucleotide reassembly methods as describedherein, including synthetic ligation polynucleotide reassembly asdescribed herein. The components can be present on the same vaccinevector, or can be included in a genetic vaccine as separate molecules.

FIG. 22A and FIG. 22B. Generation of vectors with multiple T cellepitopes. Shown here are two different strategies for generating vectorsthat contain multiple T cell epitopes obtained, for example, by directedevolution. In FIG. 60A, each individual non-stochastically generatedepitope-encoding gene is linked to a single promoter, and multiplepromoter-epitope gene constructs can be placed in a single vector. Thescheme shown, described &/or referenced herein (including incorporatedby reference) involves linking multiple epitope-encoding genes to asingle promoter.

FIG. 23. Generation of optimized genetic vaccines by directed evolution.Shown here is a diagram of the application of directed evolution to thegeneration of optimized genetic vaccines. Different forms ofpolynucleotides having known functional properties (e.g., regulatory,coding, and the like) are evolved and screened to identify variants thatexhibit improved properties for use as genetic vaccines.

FIG. 24. Recursive application of directed evolution and selection ofevolved promoter sequences as an example of flow cytometry-basedscreening methods. Shown here is a diagram of flow cytometry-basedscreening methods (FACS) for selection of optimized promoter sequencesevolved using recursive applications of the directed evolution methodsas described herein. A cytomegalovirus (CMV) promoter is used forillustrative purposes.

FIG. 25. An apparatus for microinjections of skin and muscle. Shown hereis an apparatus that is suitable for microinjection of genetic vaccinesand other reagents into tissue such as skin and muscle. The apparatus isparticularly useful for screening large numbers of agents in vivo, beingbased on a 96-well format. The tips of the apparatus are movable toallow adjustment so that the tips fit into a microtiter plate. Afterobtaining a reagent of interest is obtained from a plate, the tips areadjusted to a distance of about 2-3 mm apart, enabling transfer of 96different samples to an area of about 1.6 cm by 2.4 cm to about 2.4 cmby 3.6 cm. If desired, the volume of each sample transferred can beelectronically controlled; typically the volumes transferred range fromabout 2 ul to about 5 ul. Each reagent can be mixed with a marker agentor dye to facilitate recognition of the injection site in the tissue.For example, gold particles of different sizes and shaped can be mixedwith the reagent of interest, and microscopy and immunohistochemistryused to identify each injection site and to study the reaction inducedby each reagent. When muscle tissue is injected, the injection site isfirst revealed by surgery.

FIG. 26. Polynucleotide reassembly. Shown in Panel A is an example ofdirected evolution. N different strains of a virus are used in thisillustration, but the technique is applicable to any single nucleic acidas well as to any nucleic acid for which different strains, species, orgene families have homologous nucleic acids that have one or morenucleotide changes compared to other homologous nucleic acids. Thedifferent variant nucleic acids are experimentally generated, preferablynon-stochastically, as described herein, and screened or selected toidentify those variants that exhibit the desired property. The directedevolution method(s) and screening can be repeated one or more times toobtain further improvement. Panel B shows that successive rounds ofdirected evolution can produce progressively enhanced properties, andthat the combination of individual beneficial mutations can lead to anenhance improvement compared to the improvement achieved by anindividual beneficial mutation.

FIG. 27. Vector for promoter evolution. Shown here is an example of avector that is useful for screening to identify improved promoters froma library of promoter nucleic acids evolved using the directed evolutionmethods as described herein. Experimentally generated putative promotersare inserted into the vector upstream of a reporter gene for whichexpression is readily detected. For many applications, it is desirablethat the product of the reporter gene be a cell surface protein so thatcells which express high levels of the reporter gene can be sorted usingflow cytometry-based cell sorting using the reporter gene product.Examples of suitable reporter genes include, for example, B7-2 andmAb179 epitopes. A polyadenylation region is typically placed downstreamof the reporter gene (SV40 polyA is illustrated). The vector can alsoinclude a second reporter gene an internal control (GFP; greenfluorescent protein); this gene is linked to a promoter (SRαp). Thevector also typically includes a selectable marker (kanamycin/neomycinresistance is shown), and origins of replication that are functional inmammalian (SV40 ori) and/or bacterial (pUC ori) cells.

FIG. 28. Iterative evolution of inducible promoters using directedevolution and flow cytometry-based selection. Shown here is a diagram ofa scheme for iterative evolution of inducible promoters using thedirected evolution methods as described herein and flow cytometry-basedselection. A library of experimentally generated (i.e. produced by oneor more directed evolution methods as described herein) promoter nucleicacids present in appropriate vectors is transfected into the cells, andthose cells which exhibit the least expression of marker antigen whengrown under uninduced conditions are selected. The vectors (&/or cellscontaining them) are recovered, and the vectors are introduced intocells (if not contained therein already), and grown under inducingconditions. Those cells that express the highest level of marker antigenare selected.

FIG. 29. Evolving a genetic vaccine vector for Oral, Intravenous,Intramuscular, Intradermal, Anal, Vaginal, or Topical Delivery.Illustrated is a strategy for screening of M13 libraries (e.g. generatedexperimentally using directed evolution as descried herein) for desiredtargeting of various tissues. The particular example shown here is aschematic diagram of a method for evolving a genetic vaccine vector forimproved oral delivery. This may comprise selecting for stability underthe acidic conditions of the stomach, and resistance to otherdegredatory factors of the digestive tract. The particular exampleillustrated relates to screening for improved oral delivery, but thesame principle applies to libraries administered by other routes,including intravenously, intramuscularly, intradermally, anally,vaginally, or topically. After delivery to a test animal, the M13 phage(or a product thereof) is recovered from the tissue of interest. Theprocedure can be repeated to obtain further optimization.

FIG. 30. An alignment of the nucleotide sequences of two human CMVstrains and one monkey strain. Shown here is an alignment of thenucleotide sequences of two human cytomegalovirus (CMV) strains and onemonkey (Rhesus) strains. This alignment is serviceable for performingnon-stochastic polynucleotide reassembly. Nucleotide sequences shared by2 sequences are in blue lettering & nucleotide sequences shared by 3sequences are in red lettering to illustrate preferred but non-limitingexamples of reassembly points.

FIG. 31. An alignment of IL-4 nucleotide sequences from 3 species(human, primate, and canine). Shown here is an alignment of the IL-4nucleotide sequences of human, dog and primate strains. This alignmentis serviceable for performing non-stochastic polynucleotide reassembly.Nucleotide sequences shared by 2 sequences are in blue lettering &nucleotide sequences shared by 3 sequences are in red lettering toillustrate preferred but non-limiting examples of reassembly points.

FIG. 32. Evolution of polypeptides by synthesizing (in vivo or in vitro)corresponding deduced polynucleotides and subjecting the deducedpolynucleotides to directed evolution and expression screeningsubsequently expressed polypeptides.

FIG. 33. Non-stochastic Reassembly of oligo-directed CpG knock-outs.Shown here is a schematic representation of the use of thenon-stochastic methods described herein to generate promoter sequencesin which unnecessary CpG sequences are deleted, potentially useful CpGsequences are added, and non-replaceable CpG sequences are identified.Additionally, other sequences (aside from the CpG sequences) can besubstituted into, added to, &/or deleted from working polynucleotides.

FIG. 34. An Example of a CTIS obtained from HbsAg polypeptide (PreS2plus S regions). Shown here is an example of a cytotoxic T-cell inducingsequence (CTIS) obtained from HBsAg polypeptide (PreS2 plus S regions).

FIG. 35. A CTIS Having Heterologous Epitopes Attached to the CytoplasmicPortion. Shown here is a CTIS having heterologous epitopes attached tothe cytoplasmic portion.

FIG. 36. Method for preparing immunogenic agonist sequences (IAS). Shownhere is a method for preparing immunogenic agonist sequences (IAS).Wild-type (WT) and mutated forms of nucleic acids encoding a polypeptideof interest are assembled and subjected to non-stochastic reassembly toobtain a nucleic acid encoding a poly-epitope region that containspotential agonist sequences.

FIG. 37. Improving Immunostimulatory Sequences (ISS) Using DirectedEvolution. Shown here is a scheme for improving immunostimulatorysequences by the directed evolution methods described herein.Oligonucleotide building blocks (e.g. synthetically generated), oligoswith known ISS, CpG containing hexamers &/or oligos containing CpGcontaining hexamers, poly A, C, G, T, etc. . . . can be assembled. Theresultant molecule(s) can then by subjected to 1 or more directedevolution methods as described herein.

FIG. 38. Screening to identify IL-12 genes that encode recombinant IL-12having an increased ability to induce T Cell proliferation. Shown hereis a diagram of a procedure by which experimentally generated molecules,e.g. non-stochastically generated libraries of human IL-12 genes can bescreened to identify evolved IL-12 genes that encode evolved forms ofIL-12 having increased ability to induce T cell proliferation.

FIG. 39. Model of induction of T cell activation or anergy by geneticvaccine vectors encoding different CD80 and/or CD86 variants. Shown hereis a model of how T cell activation or anergy can be induced by geneticvaccine vectors that encode different B7-1 (CD80) and/or B7-2 (CD86)variants.

FIG. 40. Screening of CD80/CD86 variants that have improved capacity toinduce T cell activation or anergy. Shown here is a method for usingdirected evolution as described herein to obtain CD80/CD86 variants thathave improved capacity to induce T cell activation or anergy.

FIG. 41. An alignment of two CMV-derived nucleotide sequences from humanand primate species. Shown here is an alignment of two CMV-derivednucleotide sequences of human and primate strains. This alignment isserviceable for performing non-stochastic polynucleotide reassembly.Nucleotide sequences shared by 2 sequences are in red lettering toillustrate preferred but non-limiting examples of reassembly points.

FIG. 42: An alignment of the IFN-gamma nucleotide sequences from human,cat, rodent species. Shown here is an alignment of the IFN-gammanucleotide sequences from human, cat, and rodent species. This alignmentis serviceable for performing non-stochastic polynucleotide reassembly.Nucleotide sequences shared by 2 sequences are in blue lettering &nucleotide sequences shared by 3 sequences are in red lettering toillustrate preferred but non-limiting examples of reassembly points.

2. DETAILED DESCRIPTION OF THE INVENTION 2.1. Definitions of Terms

In order to facilitate understanding of the examples provided herein,certain frequently occurring methods and/or terms will be described.

The term “agent” is used herein to denote a chemical compound, a mixtureof chemical compounds, an array of spatially localized compounds (e.g.,a VLSIPS peptide array, polynucleotide array, and/or combinatorial smallmolecule array), biological macromolecule, a bacteriophage peptidedisplay library, a bacteriophage antibody (e.g., scFv) display library,a polysome peptide display library, or an extract made from biologicalmaterials such as bacteria, plants, fungi, or animal (particularmammalian) cells or tissues. Agents are evaluated for potential activityas anti-neoplastics, anti-inflammatories or apoptosis modulators byinclusion in screening assays described herein below. Agents areevaluated for potential activity as specific protein interactioninhibitors (i.e., an agent which selectively inhibits a bindinginteraction between two predetermined polypeptides but which does notsubstantially interfere with cell viability) by inclusion in screeningassays described hereinbelow.

An “ambiguous base requirement” in a restriction site refers to anucleotide base requirement that is not specified to the fullest extent,i.e. that is not a specific base (such as, in a non-limitingexemplification, a specific base selected from A, C, G, and T), butrather may be any one of at least two or more bases. Commonly acceptedabbreviations that are used in the art as well as herein to representambiguity in bases include the following: R=G or A; Y=C or T; M=A or C;K=G or T; S=G or C; W=A or T; H=A or C or T; B=G or T or C; V=G or C orA; D=G or A or T; N=A or C or G or T.

“Alignment” with respect to molecular sequences is a way to determinesimilarity between 2 or more sequences. Optimal alignment of sequencesfor comparison can be conducted, e.g., by the local homology algorithmof Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homologyalignment algorithm of Needleman & Wunsch, J Mol. Biol. 48:443 (1970),by the search for similarity method of Pearson & Lipman, Proc. Nat'l.Acad. Sci. USA 85:2444 (1988); by computerized implementations of thesealgorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin GeneticsSoftware Package, Genetics Computer Group, 575 Science Dr., Madison,Wis.), or by visual inspection (see generally Ausubel et al., infra).

One example of an algorithm that is suitable for determining percentsequence identity and sequence similarity is the BLAST algorithm, whichis described in Altschul et al., J Mol Biol. 215:403-410 (1990).Software for performing BLAST analyses is publicly available through theNational Center for Biotechnology Information(http://www.ncbl.nlm.nih.gov/). This algorithm involves firstidentifying high scoring sequence pairs (HSPs) by identifying shortwords of length W in the query sequence, which either match or satisfysome positive-valued threshold score T when aligned with a word of thesame length in a database sequence. T is referred to as the neighborhoodword score threshold (Altschul et al., supra). These initialneighborhood word hits act as seeds for initiating searches to findlonger HSPs containing them. The word hits are then extended in bothdirections along each sequence for as far as the cumulative alignmentscore can be increased. Cumulative scores are calculated using, fornucleotide sequences, the parameters M (reward score for a pair ofmatching residues; always >0) and N (penalty score for mismatchingresidues; always <0). For amino acid sequences, a scoring matrix is usedto calculate the cumulative score. Extension of the word hits in eachdirection are halted when: the cumulative alignment score falls off bythe quantity X from its maximum achieved value; the cumulative scoregoes to zero or below, due to the accumulation of one or morenegative-scoring residue alignments; or the end of either sequence isreached.

The BLAST algorithm parameters W, T, and X determine the sensitivity andspeed of the alignment. The BLASTN program (for nucleotide sequences)uses as defaults a wordlength (W) of 11, an expectation (E) of 10, acutoff of 100, M=5, N=−4, and a comparison of both strands. For aminoacid sequences, the BLASTP program uses as defaults a wordlength (W) of3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (seeHenikoff & Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915).

In addition to calculating percent sequence identity, the BLASTalgorithm also performs a statistical analysis of the similarity betweentwo sequences (see, e.g., Karlin & Altschul (1993) Proc. Nat'l. Acad.Sci. USA 90:5873-5787). One measure of similarity provided by the BLASTalgorithm is the smallest sum probability (P(N)), which provides anindication of the probability by which a match between two nucleotide oramino acid sequences would occur by chance. For example, a nucleic acidis considered similar to a reference sequence if the smallest sumprobability in a comparison of the test nucleic acid to the referencenucleic acid is less than about 0.1, more preferably less than about0.01, and most preferably less than about 0.001.

Another indication that two nucleic acid sequences are substantiallyidentical is that the two molecules hybridize to each other understringent conditions. The phrase “hybridizing specifically to”, refersto the binding, duplexing, or hybridizing of a molecule only to aparticular nucleotide sequence under stringent conditions when thatsequence is present in a complex mixture (e.g., total cellular) DNA orRNA. “Bind(s) substantially” refers to complementary hybridizationbetween a probe nucleic acid and a target nucleic acid and embracesminor mismatches that can be accommodated by reducing the stringency ofthe hybridization media to achieve the desired detection of the targetpolynucleotide sequence.

The term “amino acid” as used herein refers to any organic compound thatcontains an amino group (—NH₂) and a carboxyl group (—COOH); preferablyeither as free groups or alternatively after condensation as part ofpeptide bonds. The “twenty naturally encoded polypeptide-formingalpha-amino acids” are understood in the art and refer to: alanine (alaor A), arginine (arg or R), asparagine (asn or N), aspartic acid (asp orD), cysteine (cys or C), gluatamic acid (glu or E), glutamine (gln orQ), glycine (gly or G), histidine (his or H), isoleucine (ile or I),leucine (leu or L), lysine (lys or K), methionine (met or M),phenylalanine (phe or F), proline (pro or P), serine (ser or S),threonine (thr or T), tryptophan (trp or W), tyrosine (tyr or Y), andvaline (val or V).

The term “amplification” means that the number of copies of apolynucleotide is increased.

The term “antibody”, as used herein, refers to intact immunoglobulinmolecules, as well as fragments of immunoglobulin molecules, such asFab, Fab′, (Fab′)₂, Fv, and SCA fragments, that are capable of bindingto an epitope of an antigen. These antibody fragments, which retain someability to selectively bind to an antigen (e.g., a polypeptide antigen)of the antibody from which they are derived, can be made using wellknown methods in the art (see, e.g., Harlow and Lane, supra), and aredescribed further, as follows.

-   -   (1) An Fab fragment consists of a monovalent antigen-binding        fragment of an antibody molecule, and can be produced by        digestion of a whole antibody molecule with the enzyme papain,        to yield a fragment consisting of an intact light chain and a        portion of a heavy chain.    -   (2) An Fab′ fragment of an antibody molecule can be obtained by        treating a whole antibody molecule with pepsin, followed by        reduction, to yield a molecule consisting of an intact light        chain and a portion of a heavy chain. Two Fab′ fragments are        obtained per antibody molecule treated in this manner.    -   (3) An (Fab′)₂ fragment of an antibody can be obtained by        treating a whole antibody molecule with the enzyme pepsin,        without subsequent reduction. A (Fab′)₂ fragment is a dimer of        two Fab′ fragments, held together by two disulfide bonds.    -   (4) An Fv fragment is defined as a genetically engineered        fragment containing the variable region of a light chain and the        variable region of a heavy chain expressed as two chains.    -   (5) An single chain antibody (“SCA”) is a genetically engineered        single chain molecule containing the variable region of a light        chain and the variable region of a heavy chain, linked by a        suitable, flexible polypeptide linker.

The term “Applied Molecular Evolution” (“AME”) means the application ofan evolutionary design algorithm to a specific, useful goal. While manydifferent library formats for AME have been reported forpolynucleotides, peptides and proteins (phage, lacI and polysomes), noneof these formats have provided for recombination by random cross-oversto deliberately create a combinatorial library.

A molecule that has a “chimeric property” is a molecule that is: 1) inpart homologous and in part heterologous to a first reference molecule;while 2) at the same time being in part homologous and in partheterologous to a second reference molecule; without 3) precluding thepossibility of being at the same time in part homologous and in partheterologous to still one or more additional reference molecules. In anon-limiting embodiment, a chimeric molecule may be prepared byassemblying a reassortment of partial molecular sequences. In anon-limiting aspect, a chimeric polynucleotide molecule may be preparedby synthesizing the chimeric polynucleotide using plurality of moleculartemplates, such that the resultant chimeric polynucleotide hasproperties of a plurality of templates.

The term “cognate” as used herein refers to a gene sequence that isevolutionarily and functionally related between species. For example,but not limitation, in the human genome the human CD4 gene is thecognate gene to the mouse 3d4 gene, since the sequences and structuresof these two genes indicate that they are highly homologous and bothgenes encode a protein which functions in signaling T cell activationthrough MHC class 1′-restricted antigen recognition.

A “comparison window,” as used herein, refers to a conceptual segment ofat least 20 contiguous nucleotide positions wherein a polynucleotidesequence may be compared to a reference sequence of at least 20contiguous nucleotides and wherein the portion of the polynucleotidesequence in the comparison window may comprise additions or deletions(i.e., gaps) of 20 percent or less as compared to the reference sequence(which does not comprise additions or deletions) for optimal alignmentof the two sequences. Optimal alignment of sequences for aligning acomparison window may be conducted by the local homology algorithm ofSmith (Smith and Waterman, Adv Appl Math, 1981; Smith and Waterman, JTeor Biol, 1981; Smith and Waterman, J Mol Biol, 1981; Smith et al, JMol Evol, 1981), by the homology alignment algorithm of Needleman(Needleman and Wuncsch, 1970), by the search of similarity method ofPearson (Pearson and Lipman, 1988), by computerized implementations ofthese algorithms (GAP, BESTFIT, FASTA, and TFASTA in the WisconsinGenetics Software Package Release 7.0, Genetics Computer Group, 575Science Dr., Madison, Wis.), or by inspection, and the best alignment(i.e., resulting in the highest percentage of homology over thecomparison window) generated by the various methods is selected.

As used herein, the term “complementarity-determining region” and “CDR”refer to the art-recognized term as exemplified by the Kabat and ChothiaCDR definitions also generally known as supervariable regions orhypervariable loops (Chothia and Lesk, 1987; Clothia et al, 1989; Kabatet al, 1987; and Tramontano et al, 1990). Variable region domainstypically comprise the amino-terminal approximately 105-115 amino acidsof a naturally-occurring immunoglobulin chain (e.g., amino acids 1-110),although variable domains somewhat shorter or longer are also suitablefor forming single-chain antibodies.

“Conservative amino acid substitutions” refer to the interchangeabilityof residues having similar side chains. For example, a group of aminoacids having aliphatic side chains is glycine, alanine, valine, leucine,and isoleucine; a group of amino acids having aliphatic-hydroxyl sidechains is serine and threonine; a group of amino acids havingamide-containing side chains is asparagine and glutamine; a group ofamino acids having aromatic side chains is phenylalanine, tyrosine, andtryptophan; a group of amino acids having basic side chains is lysine,arginine, and histidine; and a group of amino acids havingsulfur-containing side chains is cysteine and methionine. Preferredconservative amino acids substitution groups are:valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine,alanine-valine, and asparagine-glutamine.

“Conservatively modified variations” of a particular polynucleotidesequence refers to those polynucleotides that encode identical oressentially identical amino acid sequences, or where the polynucleotidedoes not encode an amino acid sequence, to essentially identicalsequences. Because of the degeneracy of the genetic code, a large numberof functionally identical nucleic acids encode any given polypeptide.For instance, the codons CGU, CGC, CGA, CGG, AGA, and AGG all encode theamino acid arginine.

Thus, at every position where an arginine is specified by a codon, thecodon can be altered to any of the corresponding codons describedwithout altering the encoded polypeptide. Such nucleic acid variationsare “silent variations,” which are one species of “conservativelymodified variations.” Every polynucleotide sequence described hereinwhich encodes a polypeptide also describes every possible silentvariation, except where otherwise noted.

One of skill will recognize that each codon in a nucleic acid (exceptAUG, which is ordinarily the only codon for methionine) can be modifiedto yield a functionally identical molecule by standard techniques.Accordingly, each “silent variation” of a nucleic acid which encodes apolypeptide is implicit in each described sequence.

Furthermore, one of skill will recognize that individual substitutions,deletions or additions which alter, add or delete a single amino acid ora small percentage of amino acids (typically less than 5%, moretypically less than 1%) in an encoded sequence are “conservativelymodified variations” where the alterations result in the substitution ofan amino acid with a chemically similar amino acid. Conservativesubstitution tables providing functionally similar amino acids are wellknown in the art. The following five groups each contain amino acidsthat are conservative substitutions for one another:

Aliphatic: Glycine (G), Alanine (A), Valine (V), Leucine (L), Isoleucine(1);

Aromatic: Phenylalanine (F), Tyrosine (Y), Tryptophan (W);

Sulfur-containing: Methionine (M), Cysteine (C);

Basic: Arginine (R), Lysine (K), Histidine (H);

Acidic: Aspartic acid (D), Glutamic acid (E), Asparagine (N), Glutamine(Q).

See also, Creighton (1984) Proteins, W.H. Freeman and Company, foradditional groupings of amino acids. In addition, individualsubstitutions, deletions or additions which alter, add or delete asingle amino acid or a small percentage of amino acids in an encodedsequence are also “conservatively modified variations”.

The term “corresponds to” is used herein to mean that a polynucleotidesequence is homologous (i.e., is identical, not strictly evolutionarilyrelated) to all or a portion of a reference polynucleotide sequence, orthat a polypeptide sequence is identical to a reference polypeptidesequence. In contradistinction, the term “complementary to” is usedherein to mean that the complementary sequence is homologous to all or aportion of a reference polynucleotide sequence. For illustration, thenucleotide sequence “TATAC” corresponds to a reference “TATAC” and iscomplementary to a reference sequence “GTATA.”

The term “cytokine” includes, for example, interleukins, interferons,chemokines, hematopoietic growth factors, tumor necrosis factors andtransforming growth factors. In general these are small molecular weightproteins that regulate maturation, activation, proliferation anddifferentiation of the cells of the immune system.

The term “degrading effective” amount refers to the amount of enzymewhich is required to process at least 50% of the substrate, as comparedto substrate not contacted with the enzyme. Preferably, at least 80% ofthe substrate is degraded.

As used herein, the term “defined sequence framework” refers to a set ofdefined sequences that are selected on a non-random basis, generally onthe basis of experimental data or structural data; for example, adefined sequence framework may comprise a set of amino acid sequencesthat are predicted to form a β-sheet structure or may comprise a leucinezipper heptad repeat motif, a zinc-finger domain, among othervariations. A “defined sequence kernal” is a set of sequences whichencompass a limited scope of variability. Whereas (1) a completelyrandom 10-mer sequence of the 20 conventional amino acids can be any of(20)¹⁰ sequences, and (2) a pseudorandom 10-mer sequence of the 20conventional amino acids can be any of (20)¹⁰ sequences but will exhibita bias for certain residues at certain positions and/or overall, (3) adefined sequence kernal is a subset of sequences if each residueposition was allowed to be any of the allowable 20 conventional aminoacids (and/or allowable unconventional amino/imino acids). A definedsequence kernal generally comprises variant and invariant residuepositions and/or comprises variant residue positions which can comprisea residue selected from a defined subset of amino acid residues), andthe like, either segmentally or over the entire length of the individualselected library member sequence. Defined sequence kernels can refer toeither amino acid sequences or polynucleotide sequences. Of illustrationand not limitation, the sequences (NNK)₁₀ and (NNM)₁₀, wherein Nrepresents A, T, G, or C; K represents G or T; and M represents A or C,are defined sequence kernels.

“Digestion” of DNA refers to catalytic cleavage of the DNA with arestriction enzyme that acts only at certain sequences in the DNA. Thevarious restriction enzymes used herein are commercially available andtheir reaction conditions, cofactors and other requirements were used aswould be known to the ordinarily skilled artisan. For analyticalpurposes, typically 1 μg of plasmid or DNA fragment is used with about 2units of enzyme in about 20 μl of buffer solution. For the purpose ofisolating DNA fragments for plasmid construction, typically 5 to 50 μgof DNA are digested with 20 to 250 units of enzyme in a larger volume.Appropriate buffers and substrate amounts for particular restrictionenzymes are specified by the manufacturer. Incubation times of about 1hour at 37° C. are ordinarily used, but may vary in accordance with thesupplier's instructions. After digestion the reaction is electrophoreseddirectly on a gel to isolate the desired fragment.

“Directional ligation” refers to a ligation in which a 5′ end and a 3′end of a polynucleotide are different enough to specify a preferredligation orientation. For example, an otherwise untreated and undigestedPCR product that has two blunt ends will typically not have a preferredligation orientation when ligated into a cloning vector digested toproduce blunt ends in its multiple cloning site; thus, directionalligation will typically not be displayed under these circumstances. Incontrast, directional ligation will typically be displayed when adigested PCR product having a 5′ EcoR I-treated end and a 3′ BamH I isligated into a cloning vector that has a multiple cloning site digestedwith EcoR I and BamH I.

The term “DNA shuffling” is used herein to indicate recombinationbetween substantially homologous but non-identical sequences, in someembodiments DNA shuffling may involve crossover via non-homologousrecombination, such as via cer/10× and/or flp/frt systems and the like.

As used in this invention, the term “epitope” refers to an antigenicdeterminant on an antigen, such as a phytase polypeptide, to which theparatope of an antibody, such as an phytase-specific antibody, binds.Antigenic determinants usually consist of chemically active surfacegroupings of molecules, such as amino acids or sugar side chains, andcan have specific three-dimensional structural characteristics, as wellas specific charge characteristics. As used herein “epitope” refers tothat portion of an antigen or other macromolecule capable of forming abinding interaction that interacts with the variable region binding bodyof an antibody. Typically, such binding interaction is manifested as anintermolecular contact with one or more amino acid residues of a CDR.

An “exogenous DNA segment”, “heterologous sequence” or a “heterologousnucleic acid”, as used herein, is one that originates from a sourceforeign to the particular host cell, or, if from the same source, ismodified from its original form. Thus, a heterologous gene in a hostcell includes a gene that is endogenous to the particular host cell, buthas been modified. Modification of a heterologous sequence in theapplications described herein typically occurs through the use ofstochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly. Thus, the terms refer to a DNAsegment which is foreign or heterologous to the cell, or homologous tothe cell but in a position within the host cell nucleic acid in whichthe element is not ordinarily found.

“Exogenous” DNA segments are expressed to yield exogenous polypeptides.

The term “gene” is used broadly to refer to any segment of DNAassociated with a biological function. Thus, genes include codingsequences and/or the regulatory sequences required for their expression.Genes also include nonexpressed DNA segments that, for example, formrecognition sequences for other proteins. Genes can be obtained from avariety of sources, including cloning from a source of interest orsynthesizing from known or predicted sequence information, and mayinclude sequences designed to have desired parameters.

An “experimentally generated (in vitro &/or in vivo) polynucleotide”(which term includes a “recombinant polynucleotide”) or an“experimentally (in vitro &/or in vivo) generated polypeptide” (whichterm includes a “experimentally generated polypeptide”) is anon-naturally occurring polynucleotide or polypeptide that includesnucleic acid or amino acid sequences, respectively, from more than onesource nucleic acid or polypeptide, which source nucleic acid orpolypeptide can be a naturally occurring nucleic acid or polypeptide, orcan itself have been subjected to mutagenesis or other type ofmodification. The source polynucleotides or polypeptides from which thedifferent nucleic acid or amino acid sequences are derived are sometimeshomologous (i.e., have, or encode a polypeptide that encodes, the sameor a similar structure and/or function), and are often from differentisolates, serotypes, strains, species, of organism or from differentdisease states, for example.

The terms “fragment”, “derivative” and “analog” when referring to areference polypeptide comprise a polypeptide which retains at least onebiological function or activity that is at least essentially same asthat of the reference polypeptide. Furthermore, the terms “fragment”,“derivative” or “analog” are exemplified by a “pro-form” molecule, suchas a low activity proprotein that can be modified by cleavage to producea mature enzyme with significantly higher activity.

A method is provided herein for producing from a template polypeptide aset of progeny polypeptides in which a “full range of single amino acidsubstitutions” is represented at each amino acid position. As usedherein, “full range of single amino acid substitutions” is in referenceto the 20 naturally encoded polypeptide-forming alpha-amino acids, asdescribed herein.

The term “gene” means the segment of DNA involved in producing apolypeptide chain; it includes regions preceding and following thecoding region (leader and trailer) as well as intervening sequences(introns) between individual coding segments (exons).

“Genetic instability”, as used herein, refers to the natural tendency ofhighly repetitive sequences to be lost through a process of reductiveevents generally involving sequence simplification through the loss ofrepeated sequences. Deletions tend to involve the loss of one copy of arepeat and everything between the repeats.

The term “heterologous” means that one single-stranded nucleic acidsequence is unable to hybridize to another single-stranded nucleic acidsequence or its complement. Thus areas of heterology means that areas ofpolynucleotides or polynucleotides have areas or regions within theirsequence which are unable to hybridize to another nucleic acid orpolynucleotide. Such regions or areas are for example areas ofmutations.

The term “homologous” or “homeologous” means that one single-strandednucleic acid sequence may hybridize to a complementary single-strandednucleic acid sequence. The degree of hybridization may depend on anumber of factors including the amount of identity between the sequencesand the hybridization conditions such as temperature and saltconcentrations as discussed later. Preferably the region of identity isgreater than about 5 bp, more preferably the region of identity isgreater than 10 bp.

An immunoglobulin light or heavy chain variable region consists of a“framework” region interrupted by three hypervariable regions, alsocalled CDR's. The extent of the framework region and CDR's have beenprecisely defined; see “Sequences of Proteins of Immunological Interest”(Kabat et al, 1987). The sequences of the framework regions of differentlight or heavy chains are relatively conserved within a specie. As usedherein, a “human framework region” is a framework region that issubstantially identical (about 85 or more, usually 90-95 or more) to theframework region of a naturally occurring human immunoglobulin. Theframework region of an antibody, that is the combined framework regionsof the constituent light and heavy chains, serves to position and alignthe CDR's. The CDR's are primarily responsible for binding to an epitopeof an antigen.

The benefits of this invention extend to “commercial applications” (orcommercial processes), which term is used to include applications incommercial industry proper (or simply industry) as well asnon-commercial commercial applications (e.g. biomedical research at anon-profit institution). Relevant applications include those in areas ofdiagnosis, medicine, agriculture, manufacturing, and academia.

The term “identical” or “identity” means that two nucleic acid sequenceshave the same sequence or a complementary sequence. Thus, “areas ofidentity” means that regions or areas of a polynucleotide or the overallpolynucleotide are identical or complementary to areas of anotherpolynucleotide or the polynucleotide.

The terms “identical” or percent “identity,” in the context of two ormore nucleic acid or polypeptide sequences, refer to two or moresequences or subsequences that are the same or have a specifiedpercentage of amino acid residues or nucleotides that are the same, whencompared and aligned for maximum correspondence, as measured using oneof the following sequence comparison algorithms or by visual inspection.

For sequence comparison, typically one sequence acts as a referencesequence to which test sequences are compared. When using a sequencecomparison algorithm, test and reference sequences are input into acomputer, subsequence coordinates are designated, if necessary, andsequence algorithm program parameters are designated. The sequencecomparison algorithm then calculates the percent sequence identity forthe test sequence(s) relative to the reference sequence, based on thedesignated program parameters.

A further indication that two nucleic acid sequences or polypeptides aresubstantially “identical” is that the polypeptide encoded by the firstnucleic acid is immunologically cross reactive with, or specificallybinds to, the polypeptide encoded by the second nucleic acid. Thus, apolypeptide is typically substantially identical to a secondpolypeptide, for example, where the two peptides differ only byconservative substitutions.

The term “isolated” means that the material is removed from its originalenvironment (e.g., the natural environment if it is naturallyoccurring). For example, a naturally-occurring polynucleotide or enzymepresent in a living animal is not isolated, but the same polynucleotideor enzyme, separated from some or all of the coexisting materials in thenatural system, is isolated. Such polynucleotides could be part of avector and/or such polynucleotides or enzymes could be part of acomposition, and still be isolated in that such vector or composition isnot part of its natural environment.

The term “isolated”, when applied to a nucleic acid or protein, denotesthat the nucleic acid or protein is essentially free of other cellularcomponents with which it is associated in the natural state. It ispreferably in a homogeneous state although it can be in either a dry oraqueous solution. Purity and homogeneity are typically determined usinganalytical chemistry techniques such as polyacrylamide gelelectrophoresis or high performance liquid chromatography. A proteinwhich is the predominant species present in a preparation issubstantially purified. In particular, an isolated gene is separatedfrom open reading frames which flank the gene and encode a protein otherthan the gene of interest.

By “isolated nucleic acid” is meant a nucleic acid, e.g., a DNA or RNAmolecule, that is not immediately contiguous with the 5′ and 3′ flankingsequences with which it normally is immediately contiguous when presentin the naturally occurring genome of the organism from which it isderived. The term thus describes, for example, a nucleic acid that isincorporated into a vector, such as a plasmid or viral vector; a nucleicacid that is incorporated into the genome of a heterologous cell (or thegenome of a homologous cell, but at a site different from that at whichit naturally occurs); and a nucleic acid that exists as a separatemolecule, e.g., a DNA fragment produced by PCR amplification orrestriction enzyme digestion, or an RNA molecule produced by in vitrotranscription. The term also describes a recombinant nucleic acid thatforms part of a hybrid gene encoding additional polypeptide sequencesthat can be used, for example, in the production of a fusion protein.

As used herein “ligand” refers to a molecule, such as a random peptideor variable segment sequence, that is recognized by a particularreceptor. As one of skill in the art will recognize, a molecule (ormacromolecular complex) can be both a receptor and a ligand. In general,the binding partner having a smaller molecular weight is referred to asthe ligand and the binding partner having a greater molecular weight isreferred to as a receptor.

“Ligation” refers to the process of forming phosphodiester bonds betweentwo double stranded nucleic acid fragments (Sambrook et al, 1982, p.146; Sambrook, 1989). Unless otherwise provided, ligation may beaccomplished using known buffers and conditions with 10 units of T4 DNAligase (“ligase”) per 0.5 μg of approximately equimolar amounts of theDNA fragments to be ligated.

As used herein, “linker” or “spacer” refers to a molecule or group ofmolecules that connects two molecules, such as a DNA binding protein anda random peptide, and serves to place the two molecules in a preferredconfiguration, e.g., so that the random peptide can bind to a receptorwith minimal steric hindrance from the DNA binding protein.

As used herein, a “molecular property to be evolved” includes referenceto molecules comprised of a polynucleotide sequence, molecules comprisedof a polypeptide sequence, and molecules comprised in part of apolynucleotide sequence and in part of a polypeptide sequence.Particularly relevant—but by no means limiting—examples of molecularproperties to be evolved include enzymatic activities at specifiedconditions, such as related to temperature; salinity; pressure; pH; andconcentration of glycerol, DMSO, detergent, &/or any other molecularspecies with which contact is made in a reaction environment. Additionalparticularly relevant—but by no means limiting—examples of molecularproperties to be evolved include stabilities—e.g. the amount of aresidual molecular property that is present after a specified exposuretime to a specified environment, such as may be encountered duringstorage.

A “multivalent antigenic polypeptide” or a “recombinant multivalentantigenic polypeptide” is a non-naturally occurring polypeptide thatincludes amino acid sequences from more than one source polypeptide,which source polypeptide is typically a naturally occurring polypeptide.At least some of the regions of different amino acid sequencesconstitute epitopes that are recognized by antibodies found in a mammalthat has been injected with the source polypeptide. The sourcepolypeptides from which the different epitopes are derived are usuallyhomologous (i.e., have the same or a similar structure and/or function),and are often from different isolates, serotypes, strains, species, oforganism or from different disease states, for example.

The term “mutations” includes changes in the sequence of a wild-type orparental nucleic acid sequence or changes in the sequence of a peptide.Such mutations may be point mutations such as transitions ortransversions. The mutations may be deletions, insertions orduplications. A mutation can also be a “chimerization”, which isexemplified in a progeny molecule that is generated to contain part orall of a sequence of one parental molecule as well as part or all of asequence of at least one other parental molecule. This inventionprovides for both chimeric polynucleotides and chimeric polypeptides.

As used herein, the degenerate “N,N,G/T” nucleotide sequence represents32 possible triplets, where “N” can be A, C, G or T.

The term “naturally-occurring” as used herein as applied to the objectrefers to the fact that an object can be found in nature. For example, apolypeptide or polynucleotide sequence that is present in an organism(including viruses bacteria, protozoa, insects, plants or mammaliantissue) that can be isolated from a source in nature and which has notbeen intentionally modified by man in the laboratory is naturallyoccurring. Generally, the term naturally occurring refers to an objectas present in a non-pathological (un-diseased) individual, such as wouldbe typical for the species.

The term “nucleic acid” refers to deoxyribonucleotides orribonucleotides and polymers thereof in either single- ordouble-stranded form. Unless specifically limited, the term encompassesnucleic acids containing known analogues of natural nucleotides whichhave similar binding properties as the reference nucleic acid and aremetabolized in a manner similar to naturally occurring nucleotides.Unless otherwise indicated, a particular nucleic acid sequence alsoimplicitly encompasses conservatively modified variants thereof (e.g.degenerate codon substitutions) and complementary sequences and as wellas the sequence explicitly indicated. Specifically, degenerate codonsubstitutions may be achieved by generating sequences in which the thirdposition of one or more selected (or all) codons is substituted withmixed-base and/or deoxyinosine residues (Batzer et al. (1991) NucleicAcid Res. 19: 5081; Ohtsuka et al. (1985) J Biol. Chem. 260: 2605-2608;Cassol et al. (1992) Rossolini et al. (1994) Mol. Cell. Probes 8:91-98). The term nucleic acid is used interchangeably with gene, cDNA,and mRNA encoded by a gene.

“Nucleic acid derived from a gene” refers to a nucleic acid for whosesynthesis the gene, or a subsequence thereof, has ultimately served as atemplate. Thus, an mRNA, a cDNA reverse transcribed from an mRNA, an RNAtranscribed from that cDNA, a DNA amplified from the cDNA, an RNAtranscribed from the amplified DNA, etc., are all derived from the geneand detection of such derived products is indicative of the presenceand/or abundance of the original gene and/or gene transcript in asample.

As used herein, a “nucleic acid molecule” is comprised of at least onebase or one base pair, depending on whether it is single-stranded ordouble-stranded, respectively. Furthermore, a nucleic acid molecule maybelong exclusively or chimerically to any group of nucleotide-containingmolecules, as exemplified by, but not limited to, the following groupsof nucleic acid molecules: RNA, DNA, genomic nucleic acids, non-genomicnucleic acids, naturally occurring and not naturally occurring nucleicacids, and synthetic nucleic acids. This includes, by way ofnon-limiting example, nucleic acids associated with any organelle, suchas the mitochondria, ribosomal RNA, and nucleic acid molecules comprisedchimerically of one or more components that are not naturally occurringalong with naturally occurring components.

Additionally, a “nucleic acid molecule” may contain in part one or morenon-nucleotide-based components as exemplified by, but not limited to,amino acids and sugars. Thus, by way of example, but not limitation, aribozyme that is in part nucleotide-based and in part protein-based isconsidered a “nucleic acid molecule”.

In addition, by way of example, but not limitation, a nucleic acidmolecule that is labeled with a detectable moiety, such as a radioactiveor alternatively a non-radioactive label, is likewise considered a“nucleic acid molecule”.

The terms “nucleic acid sequence coding for” or a “DNA coding sequenceof” or a “nucleotide sequence encoding” a particular enzyme—as well asother synonymous terms—refer to a DNA sequence which is transcribed andtranslated into an enzyme when placed under the control of appropriateregulatory sequences. A “promotor sequence” is a DNA regulatory regioncapable of binding RNA polymerase in a cell and initiating transcriptionof a downstream (3′ direction) coding sequence. The promoter is part ofthe DNA sequence. This sequence region has a start codon at its 3′terminus. The promoter sequence does include the minimum number of baseswhere elements necessary to initiate transcription at levels detectableabove background. However, after the RNA polymerase binds the sequenceand transcription is initiated at the start codon (3′ terminus with apromoter), transcription proceeds downstream in the 3′ direction. Withinthe promotor sequence will be found a transcription initiation site(conveniently defined by mapping with nuclease S1) as well as proteinbinding domains (consensus sequences) responsible for the binding of RNApolymerase.

The terms “nucleic acid encoding an enzyme (protein)” or “DNA encodingan enzyme (protein)” or “polynucleotide encoding an enzyme (protein)”and other synonymous terms encompasses a polynucleotide which includesonly coding sequence for the enzyme as well as a polynucleotide whichincludes additional coding and/or non-coding sequence.

In one preferred embodiment, a “specific nucleic acid molecule species”is defined by its chemical structure, as exemplified by, but not limitedto, its primary sequence. In another preferred embodiment, a specific“nucleic acid molecule species” is defined by a function of the nucleicacid species or by a function of a product derived from the nucleic acidspecies. Thus, by way of non-limiting example, a “specific nucleic acidmolecule species” may be defined by one or more activities or propertiesattributable to it, including activities or properties attributable itsexpressed product.

The instant definition of “assembling a working nucleic acid sample intoa nucleic acid library” includes the process of incorporating a nucleicacid sample into a vector-based collection, such as by ligation into avector and transformation of a host. A description of relevant vectors,hosts, and other reagents as well as specific non-limiting examplesthereof are provided hereinafter. The instant definition of “assemblinga working nucleic acid sample into a nucleic acid library” also includesthe process of incorporating a nucleic acid sample into anon-vector-based collection, such as by ligation to adaptors. Preferablythe adaptors can anneal to PCR primers to facilitate amplification byPCR.

Accordingly, in a non-limiting embodiment, a “nucleic acid library” iscomprised of a vector-based collection of one or more nucleic acidmolecules. In another preferred embodiment a “nucleic acid library” iscomprised of a non-vector-based collection of nucleic acid molecules. Inyet another preferred embodiment a “nucleic acid library” is comprisedof a combined collection of nucleic acid molecules that is in partvector-based and in part non-vector-based. Preferably, the collection ofmolecules comprising a library is searchable and separable according toindividual nucleic acid molecule species.

The present invention provides a “nucleic acid construct” oralternatively a “nucleotide construct” or alternatively a “DNAconstruct”. The term “construct” is used herein to describe a molecule,such as a polynucleotide (e.g., a phytase polynucleotide) may optionallybe chemically bonded to one or more additional molecular moieties, suchas a vector, or parts of a vector. In a specific—but by no meanslimiting—aspect, a nucleotide construct is exemplified by a DNAexpression constructs suitable for the transformation of a host cell.

An “oligonucleotide” (or synonymously an “oligo”) refers to either asingle stranded polydeoxynucleotide or two complementarypolydeoxynucleotide strands which may be chemically synthesized. Suchsynthetic oligonucleotides may or may not have a 5′ phosphate. Thosethat do not will not ligate to another oligonucleotide without adding aphosphate with an ATP in the presence of a kinase. A syntheticoligonucleotide will ligate to a fragment that has not beendephosphorylated. To achieve polymerase-based amplification (such aswith PCR), a “32-fold degenerate oligonucleotide that is comprised of,in series, at least a first homologous sequence, a degenerate N,N,G/Tsequence, and a second homologous sequence” is mentioned. As used inthis context, “homologous” is in reference to homology between the oligoand the parental polynucleotide that is subjected to thepolymerase-based amplification.

A nucleic acid is “operably linked” when it is placed into a functionalrelationship with another nucleic acid sequence. For instance, apromoter or enhancer is operably linked to a coding sequence if itincreases the transcription of the coding sequence.

As used herein, the term “operably linked” refers to a linkage ofpolynucleotide elements in a functional relationship. A nucleic acid is“operably linked” when it is placed into a functional relationship withanother nucleic acid sequence. For instance, a promoter or enhancer isoperably linked to a coding sequence if it affects the transcription ofthe coding sequence. Operably linked means that the DNA sequences beinglinked are typically contiguous and, where necessary to join two proteincoding regions, contiguous and in reading frame. However, sinceenhancers generally function when separated from the promoter by severalkilobases and intronic sequences may be of variable lengths, somepolynucleotide elements may be operably linked but not contiguous.

A coding sequence is “operably linked to” another coding sequence whenRNA polymerase will transcribe the two coding sequences into a singlemRNA, which is then translated into a single polypeptide having aminoacids derived from both coding sequences. The coding sequences need notbe contiguous to one another so long as the expressed sequences areultimately processed to produce the desired protein.

As used herein the term “parental polynucleotide set” is a set comprisedof one or more distinct polynucleotide species. Usually this term isused in reference to a progeny polynucleotide set which is preferablyobtained by mutagenization of the parental set, in which case the terms“parental”, “starting” and “template” are used interchangeably.

As used herein the term “physiological conditions” refers totemperature, pH, ionic strength, viscosity, and like biochemicalparameters which are compatible with a viable organism, and/or whichtypically exist intracellularly in a viable cultured yeast cell ormammalian cell. For example, the intracellular conditions in a yeastcell grown under typical laboratory culture conditions are physiologicalconditions. Suitable in vitro reaction conditions for in vitrotranscription cocktails are generally physiological conditions. Ingeneral, in vitro physiological conditions comprise 50-200 mM NaCl orKCl, pH 6.5-8.5, 20-45° C. and 0.001-10 mM divalent cation (e.g., Mg⁺⁺,Ca⁺⁺); preferably about 150 mM NaCl or KCl, pH 7.2-7.6, 5 mM divalentcation, and often include 0.01-1.0 percent nonspecific protein (e.g.,BSA). A non-ionic detergent (Tween, NP-40, Triton X-100) can often bepresent, usually at about 0.001 to 2%, typically 0.05-0.2% (v/v).Particular aqueous conditions may be selected by the practitioneraccording to conventional methods. For general guidance, the followingbuffered aqueous conditions may be applicable: 10-250 mM NaCl, 5-50 mMTris HCl, pH 5-8, with optional addition of divalent cation(s) and/ormetal chelators and/or non-ionic detergents and/or membrane fractionsand/or anti-foam agents and/or scintillants.

Standard convention (5′ to 3′) is used herein to describe the sequenceof double stranded polynucleotides.

The term “population” as used herein means a collection of componentssuch as polynucleotides, portions or polynucleotides or proteins. A“mixed population: means a collection of components which belong to thesame family of nucleic acids or proteins (i.e., are related) but whichdiffer in their sequence (i.e., are not identical) and hence in theirbiological activity.

A molecule having a “pro-form” refers to a molecule that undergoes anycombination of one or more covalent and noncovalent chemicalmodifications (e.g. glycosylation, proteolytic cleavage, dimerization oroligomerization, temperature-induced or pH-induced conformationalchange, association with a co-factor, etc.) en route to attain a moremature molecular form having a property difference (e.g. an increase inactivity) in comparison with the reference pro-form molecule. When twoor more chemical modification (e.g. two proteolytic cleavages, or aproteolytic cleavage and a deglycosylation) can be distinguished enroute to the production of a mature molecule, the reference precursormolecule may be termed a “pre-pro-form” molecule.

As used herein, the term “pseudorandom” refers to a set of sequencesthat have limited variability, such that, for example, the degree ofresidue variability at another position, but any pseudorandom positionis allowed some degree of residue variation, however circumscribed.

The term “purified” denotes that a nucleic acid or protein gives rise toessentially one band in an electrophoretic gel. Particularly, it meansthat the nucleic acid or protein is at least about 50% pure, morepreferably at least about 85% pure, and most preferably at least about99% pure.

“Quasi-repeated units”, as used herein, refers to the repeats to bere-assorted and are by definition not identical. Indeed the method isproposed not only for practically identical encoding units produced bymutagenesis of the identical starting sequence, but also thereassortment of similar or related sequences which may divergesignificantly in some regions. Nevertheless, if the sequences containsufficient homologies to be reasserted by this approach, they can bereferred to as “quasi-repeated” units.

As used herein “random peptide library” refers to a set ofpolynucleotide sequences that encodes a set of random peptides, and tothe set of random peptides encoded by those polynucleotide sequences, aswell as the fusion proteins contain those random peptides.

As used herein, “random peptide sequence” refers to an amino acidsequence composed of two or more amino acid monomers and constructed bya stochastic or random process. A random peptide can include frameworkor scaffolding motifs, which may comprise invariant sequences.

As used herein, “receptor” refers to a molecule that has an affinity fora given ligand. Receptors can be naturally occurring or syntheticmolecules. Receptors can be employed in an unaltered state or asaggregates with other species. Receptors can be attached, covalently ornon-covalently, to a binding member, either directly or via a specificbinding substance. Examples of receptors include, but are not limitedto, antibodies, including monoclonal antibodies and antisera reactivewith specific antigenic determinants (such as on viruses, cells, orother materials), cell membrane receptors, complex carbohydrates andglycoproteins, enzymes, and hormone receptors.

The term “recombinant” when used with reference to a cell indicates thatthe cell replicates a heterologous nucleic acid, or expresses a peptideor protein encoded by a heterologous nucleic acid. Recombinant cells cancontain genes that are not found within the native (non-recombinant)form of the cell. Recombinant cells can also contain genes found in thenative form of the cell wherein the genes are modified and re-introducedinto the cell by artificial means. The term also encompasses cells thatcontain a nucleic acid endogenous to the cell that has been modifiedwithout removing the nucleic acid from the cell; such modificationsinclude those obtained by gene replacement, site-specific mutation, andrelated techniques.

“Recombinant enzymes” refer to enzymes produced by recombinant DNAtechniques, i.e., produced from cells transformed by an exogenous DNAconstruct encoding the desired enzyme. “Synthetic” enzymes are thoseprepared by chemical synthesis.

A “recombinant expression cassette” or simply an “expression cassette”is a nucleic acid construct, generated recombinantly or synthetically,with nucleic acid elements that are capable of effecting expression of astructural gene in hosts compatible with such sequences. Expressioncassettes include at least promoters and optionally, transcriptiontermination signals. Typically, the recombinant expression cassetteincludes a nucleic acid to be transcribed (e.g., a nucleic acid encodinga desired polypeptide), and a promoter. Additional factors necessary orhelpful in effecting expression may also be used as described herein.For example, an expression cassette can also include nucleotidesequences that encode a signal sequence that directs secretion of anexpressed protein from the host cell. Transcription termination signals,enhancers, and other nucleic acid sequences that influence geneexpression, can also be included in an expression cassette.

The term “related polynucleotides” means that regions or areas of thepolynucleotides are identical and regions or areas of thepolynucleotides are heterologous.

“Reductive reassortment”, as used herein, refers to the increase inmolecular diversity that is accrued through deletion (and/or insertion)events that are mediated by repeated sequences.

The following terms are used to describe the sequence relationshipsbetween two or more polynucleotides: “reference sequence,” “comparisonwindow,” “sequence identity,” “percentage of sequence identity,” and“substantial identity.”

A “reference sequence” is a defined sequence used as a basis for asequence comparison; a reference sequence may be a subset of a largersequence, for example, as a segment of a full-length cDNA or genesequence given in a sequence listing, or may comprise a complete cDNA orgene sequence. Generally, a reference sequence is at least 20nucleotides in length, frequently at least 25 nucleotides in length, andoften at least 50 nucleotides in length. Since two polynucleotides mayeach (1) comprise a sequence (i.e., a portion of the completepolynucleotide sequence) that is similar between the two polynucleotidesand (2) may further comprise a sequence that is divergent between thetwo polynucleotides, sequence comparisons between two (or more)polynucleotides are typically performed by comparing sequences of thetwo polynucleotides over a “comparison window” to identify and comparelocal regions of sequence similarity.

“Repetitive Index (RI)”, as used herein, is the average number of copiesof the quasi-repeated units contained in the cloning vector.

The term “restriction site” refers to a recognition sequence that isnecessary for the manifestation of the action of a restriction enzyme,and includes a site of catalytic cleavage. It is appreciated that a siteof cleavage may or may not be contained within a portion of arestriction site that comprises a low ambiguity sequence (i.e. asequence containing the principal determinant of the frequency ofoccurrence of the restriction site). Thus, in many cases, relevantrestriction sites contain only a low ambiguity sequence with an internalcleavage site (e.g. G/AATTC in the EcoR I site) or an immediatelyadjacent cleavage site (e.g. /CCWGG in the EcoR II site). In othercases, relevant restriction enzymes [e.g. the Eco57 I site orCTGAAG(16/14)] contain a low ambiguity sequence (e.g. the CTGAAGsequence in the Eco57 I site) with an external cleavage site (e.g. inthe N₁₆ portion of the Eco57 I site). When an enzyme (e.g. a restrictionenzyme) is said to “cleave” a polynucleotide, it is understood to meanthat the restriction enzyme catalyzes or facilitates a cleavage of apolynucleotide.

The term “screening” describes, in general, a process that identifiesoptimal antigens. Several properties of the antigen can be used inselection and screening including antigen expression, folding,stability, immunogenicity and presence of epitopes from several relatedantigens. Selection is a form of screening in which identification andphysical separation are achieved simultaneously by expression of aselection marker, which, in some genetic circumstances, allows cellsexpressing the marker to survive while other cells die (or vice versa).Screening markers include, for example, luciferase, beta-galactosidaseand green fluorescent protein. Selection markers include drug and toxinresistance genes, and the like. Because of limitations in studyingprimary immune responses in vitro, in vivo studies are particularlyuseful screening methods. In these studies, the antigens are firstintroduced to test animals, and the immune responses are subsequentlystudied by analyzing protective immune responses or by studying thequality or strength of the induced immune response using lymphoid cellsderived from the immunized animal. Although spontaneous selection canand does occur in the course of natural evolution, in the presentmethods selection is performed by man.

In a non-limiting aspect, a “selectable polynucleotide” is comprised ofa 5′ terminal region (or end region), an intermediate region (i.e. aninternal or central region), and a 3′ terminal region (or end region).As used in this aspect, a 5′ terminal region is a region that is locatedtowards a 5′ polynucleotide terminus (or a 5′ polynucleotide end); thusit is either partially or entirely in a 5′ half of a polynucleotide.Likewise, a 3′ terminal region is a region that is located towards a 3′polynucleotide terminus (or a 3′ polynucleotide end); thus it is eitherpartially or entirely in a 3′ half of a polynucleotide. As used in thisnon-limiting exemplification, there may be sequence overlap between anytwo regions or even among all three regions.

The term “sequence identity” means that two polynucleotide sequences areidentical (i.e., on a nucleotide-by-nucleotide basis) over the window ofcomparison. The term “percentage of sequence identity” is calculated bycomparing two optimally aligned sequences over the window of comparison,determining the number of positions at which the identical nucleic acidbase (e.g., A, T, C, G, U, or I) occurs in both sequences to yield thenumber of matched positions, dividing the number of matched positions bythe total number of positions in the window of comparison (i.e., thewindow size), and multiplying the result by 100 to yield the percentageof sequence identity. This “substantial identity”, as used herein,denotes a characteristic of a polynucleotide sequence, wherein thepolynucleotide comprises a sequence having at least 80 percent sequenceidentity, preferably at least 85 percent identity, often 90 to 95percent sequence identity, and most commonly at least 99 percentsequence identity as compared to a reference sequence of a comparisonwindow of at least 25-50 nucleotides, wherein the percentage of sequenceidentity is calculated by comparing the reference sequence to thepolynucleotide sequence which may include deletions or additions whichtotal 20 percent or less of the reference sequence over the window ofcomparison.

As known in the art “similarity” between two enzymes is determined bycomparing the amino acid sequence and its conserved amino acidsubstitutes of one enzyme to the sequence of a second enzyme. Similaritymay be determined by procedures which are well-known in the art, forexample, a BLAST program (Basic Local Alignment Search Tool at theNational Center for Biological Information).

As used herein, the term “single-chain antibody” refers to a polypeptidecomprising a V_(H) domain and a V_(L) domain in polypeptide linkage,generally linked via a spacer peptide (e.g., [Gly-Gly-Gly-Gly-Ser]_(x)),and which may comprise additional amino acid sequences at the amino-and/or carboxy-termini. For example, a single-chain antibody maycomprise a tether segment for linking to the encoding polynucleotide. Asan example, a scFv is a single-chain antibody. Single-chain antibodiesare generally proteins consisting of one or more polypeptide segments ofat least 10 contiguous amino substantially encoded by genes of theimmunoglobulin superfamily (e.g., see Williams and Barclay, 1989, pp.361-368, which is incorporated herein by reference), most frequentlyencoded by a rodent, non-human primate, avian, porcine bovine, ovine,goat, or human heavy chain or light chain gene sequence. A functionalsingle-chain antibody generally contains a sufficient portion of animmunoglobulin superfamily gene product so as to retain the property ofbinding to a specific target molecule, typically a receptor or antigen(epitope).

The phrase “specifically (or selectively) binds to an antibody” or“specifically (or selectively) immunoreactive with”, when referring to aprotein or peptide, refers to a binding reaction which is determinativeof the presence of the protein, or an epitope from the protein, in thepresence of a heterogeneous population of proteins and other biologics.Thus, under designated immunoassay conditions, the specified antibodiesbind to a particular protein and do not bind in a significant amount toother proteins present in the sample. The antibodies raised against amultivalent antigenic polypeptide will generally bind to the proteinsfrom which one or more of the epitopes were obtained. Specific bindingto an antibody under such conditions may require an antibody that isselected for its specificity for a particular protein. A variety ofimmunoassay formats may be used to select antibodies specificallyimmunoreactive with a particular protein. For example, solid-phase ELISAimmunoassays, Western blots, or immunohistochemistry are routinely usedto select monoclonal antibodies specifically immunoreactive with aprotein. See Harlow and Lane (1988) Antibodies, A Laboratory Manual,Cold Spring Harbor Publications, New York “Harlow and Lane”), for adescription of immunoassay formats and conditions that can be used todetermine specific immunoreactivity. Typically a specific or selectivereaction will be at least twice background signal or noise and moretypically more than 10 to 100 times background.

The members of a pair of molecules (e.g., an antibody-antigen pair or anucleic acid pair) are said to “specifically bind” to each other if theybind to each other with greater affinity than to other, non-specificmolecules. For example, an antibody raised against an antigen to whichit binds more efficiently than to a non-specific protein can bedescribed as specifically binding to the antigen. (Similarly, a nucleicacid probe can be described as specifically binding to a nucleic acidtarget if it forms a specific duplex with the target by base pairinginteractions (see above).)

A “specific binding affinity” between two molecules, for example, aligand and a receptor, means a preferential binding of one molecule foranother in a mixture of molecules. The binding of the molecules can beconsidered specific if the binding affinity is about 1×10⁴ M⁻¹ to about1×10⁶M⁻¹ or greater.

“Specific hybridization” is defined herein as the formation of hybridsbetween a first polynucleotide and a second polynucleotide (e.g., apolynucleotide having a distinct but substantially identical sequence tothe first polynucleotide), wherein substantially unrelatedpolynucleotide sequences do not form hybrids in the mixture.

The term “specific polynucleotide” means a polynucleotide having certainend points and having a certain nucleic acid sequence. Twopolynucleotides wherein one polynucleotide has the identical sequence asa portion of the second polynucleotide but different ends comprises twodifferent specific polynucleotides.

The T_(m) is the temperature (under defined ionic strength and pH) atwhich 50% of the target sequence hybridizes to a perfectly matchedprobe. Very stringent conditions are selected to be equal to the T_(m)for a particular probe. An example of stringent hybridization conditionsfor hybridization of complementary nucleic acids which have more than100 complementary residues on a filter in a Southern or Northern blot is50% formamide with 1 mg of heparin at 42° C., with the hybridizationbeing carried out overnight.

“Stringent hybridization conditions” means hybridization will occur onlyif there is at least 90% identity, preferably at least 95% identity andmost preferably at least 97% identity between the sequences. SeeSambrook et al, 1989, which is hereby incorporated by reference in itsentirety.

An example of highly “stringent” wash conditions is 0.15M NaCl at 72° C.for about 15 minutes. An example of stringent wash conditions is a0.2×SSC wash at 65° C. for 15 minutes (see, Sambrook, infra., for adescription of SSC buffer). Often, a high stringency wash is preceded bya low stringency wash to remove background probe signal. An examplemedium stringency wash for a duplex of, e.g., more than 100 nucleotides,is 1×SSC at 45° C. for 15 minutes. An example low stringency wash for aduplex of, e.g., more than 100 nucleotides, is 4-6×SSC at 40° C. for 15minutes. For short probes (e.g., about 10 to 50 nucleotides), stringentconditions typically involve salt concentrations of less than about 1.0M Na⁺ ion, typically about 0.01 to 1.0 M Na⁺ ion concentration (or othersalts) at pH 7.0 to 8.3, and the temperature is typically at least about30° C. Stringent conditions can also be achieved with the addition ofdestabilizing agents such as formamide. In general, a signal to noiseratio of 2× (or higher) than that observed for an unrelated probe in theparticular hybridization assay indicates detection of a specifichybridization. Nucleic acids which do not hybridize to each other understringent conditions are still substantially identical if thepolypeptides which they encode are substantially identical. This occurs,e.g., when a copy of a nucleic acid is created using the maximum codondegeneracy permitted by the genetic code.

“Stringent hybridization conditions” and “stringent hybridization washconditions” in the context of nucleic acid hybridization experimentssuch as Southern and northern hybridizations are sequence dependent, andare different under different environmental parameters. Longer sequenceshybridize specifically at higher temperatures.

An extensive guide to the hybridization of nucleic acids is found inTijssen (1993) Laboratory Techniques in Biochemistry and MolecularBiology—Hybridization with Nucleic Acid Probes part I chapter 2“Overview of principles of hybridization and the strategy of nucleicacid probe assays”, Elsevier, N.Y. Generally, highly stringenthybridization and wash conditions are selected to be about 5° C. lowerthan the thermal melting point (T_(m)) for the specific sequence at adefined ionic strength and pH. Typically, under “stringent conditions” aprobe will hybridize to its target subsequence, but to no othersequences.

Also included in the invention are polypeptides having sequences thatare “substantially identical” to the sequence of a phytase polypeptide,such as one of SEQ ID 1. A “substantially identical” amino acid sequenceis a sequence that differs from a reference sequence only byconservative amino acid substitutions, for example, substitutions of oneamino acid for another of the same class (e.g., substitution of onehydrophobic amino acid, such as isoleucine, valine, leucine, ormethionine, for another, or substitution of one polar amino acid foranother, such as substitution of arginine for lysine, glutamic acid foraspartic acid, or glutamine for asparagine).

The phrase “substantially identical,” in the context of two nucleicacids or polypeptides, refers to two or more sequences or subsequencesthat have at least 60%, preferably 80%, most preferably 90-95%nucleotide or amino acid residue identity, when compared and aligned formaximum correspondence, as measured using one of the following sequencecomparison algorithms or by visual inspection. Preferably, thesubstantial identity exists over a region of the sequences that is atleast about 50 residues in length, more preferably over a region of atleast about 100 residues, and most preferably the sequences aresubstantially identical over at least about 150 residues. In someembodiments, the sequences are substantially identical over the entirelength of the coding regions.

A “subsequence” refers to a sequence of nucleic acids or amino acidsthat comprise a part of a longer sequence of nucleic acids or aminoacids (e.g., polypeptide) respectively.

Additionally a “substantially identical” amino acid sequence is asequence that differs from a reference sequence or by one or morenon-conservative substitutions, deletions, or insertions, particularlywhen such a substitution occurs at a site that is not the active sitethe molecule, and provided that the polypeptide essentially retains itsbehavioural properties. For example, one or more amino acids can bedeleted from a phytase polypeptide, resulting in modification of thestructure of the polypeptide, without significantly altering itsbiological activity. For example, amino- or carboxyl-terminal aminoacids that are not required for phytase biological activity can beremoved. Such modifications can result in the development of smalleractive phytase polypeptides.

The present invention provides a “substantially pure enzyme”. The term“substantially pure enzyme” is used herein to describe a molecule, suchas a polypeptide (e.g., a phytase polypeptide, or a fragment thereof)that is substantially free of other proteins, lipids, carbohydrates,nucleic acids, and other biological materials with which it is naturallyassociated. For example, a substantially pure molecule, such as apolypeptide, can be at least 60%, by dry weight, the molecule ofinterest. The purity of the polypeptides can be determined usingstandard methods including, e.g., polyacrylamide gel electrophoresis(e.g., SDS-PAGE), column chromatography (e.g., high performance liquidchromatography (HPLC)), and amino-terminal amino acid sequence analysis.

As used herein, “substantially pure” means an object species is thepredominant species present (i.e., on a molar basis it is more abundantthan any other individual macromolecular species in the composition),and preferably substantially purified fraction is a composition whereinthe object species comprises at least about 50 percent (on a molarbasis) of all macromolecular species present. Generally, a substantiallypure composition will comprise more than about 80 to 90 percent of allmacromolecular species present in the composition. Most preferably, theobject species is purified to essential homogeneity (contaminant speciescannot be detected in the composition by conventional detection methods)wherein the composition consists essentially of a single macromolecularspecies. Solvent species, small molecules (<500 Daltons), and elementalion species are not considered macromolecular species.

As used herein, the term “variable segment” refers to a portion of anascent peptide which comprises a random, pseudorandom, or defined kemalsequence. A variable segment” refers to a portion of a nascent peptidewhich comprises a random pseudorandom, or defined kernal sequence. Avariable segment can comprise both variant and invariant residuepositions, and the degree of residue variation at a variant residueposition may be limited: both options are selected at the discretion ofthe practitioner. Typically, variable segments are about 5 to 20 aminoacid residues in length (e.g., 8 to 10), although variable segments maybe longer and may comprise antibody portions or receptor proteins, suchas an antibody fragment, a nucleic acid binding protein, a receptorprotein, and the like.

The term “wild-type” means that the polynucleotide does not comprise anymutations. A “wild type” protein means that the protein will be activeat a level of activity found in nature and will comprise the amino acidsequence found in nature.

The term “working”, as in “working sample”, for example, is simply asample with which one is working. Likewise, a “working molecule”, forexample is a molecule with which one is working.

2.2. General Considerations & Formats for Recombination

Component Modules Provides Genetic Vaccine with the Acquisition of orImprovement in a Useful Property or Characteristic.

The present invention provides multicomponent genetic vaccines thatinclude one or more component modules, each of which provides thegenetic vaccine with the acquisition of or an improvement in a propertyor characteristic useful in genetic vaccination.

The invention provides significant advantages over previously usedgenetic vaccines. Through use of a multicomponent vaccine, one canobtain an immune response that is particularly effective for aparticular application. A multicomponent genetic vaccine can, forexample, contain a component that is optimized for optimal antigenexpression, as well as a component that confers improved activation ofcytotoxic T lymphocytes (CTLs) by enhancing the presentation of theantigen on dendritic cell MHC Class I molecules. Additional examples aredescribed herein.

The invention provides a new approach to vaccine development, which istermed “antigen library immunization.” No other technologies areavailable for generating libraries of related antigens or optimizingknown protective antigens. The most powerful previously existing methodsfor identification of vaccine antigens, such as high throughputsequencing or expression library immunization, only explore the sequencespace provided by the pathogen genome. These approaches are likely to beinsufficient, because they generally only target single pathogenstrains, and because natural evolution has directed pathogens todownregulate their own immunogenicity. In contrast, the immunizationprotocols of the invention, which use experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) antigen libraries, provide a means to identify novelantigen sequences. Those antigens that are most protective can beselected from these pools by in vivo challenge models. Antigen libraryimmunization dramatically expands the diversity of available immunogensequences, and therefore, these antigen chimera libraries can alsoprovide means to defend against newly emerging pathogen variants of thefuture. The methods of the invention enable the identification ofindividual chimeric antigens that provide efficient protection against avariety of existing pathogens, providing improved vaccines for troopsand civilian populations.

The methods of the invention provide an evolution-based approach, suchas stochastic (e.g. polynucleotide shuffling & interrupted synthesis)and non-stochastic polynucleotide reassembly in particular, that is anoptimal approach to improve the immunogenicity of many types ofantigens. For example, the methods provide means of obtaining optimizedcancer antigens useful for preventing and treating malignant diseases.Furthermore, an increasing number of self-antigens, causing autoimmunediseases, and allergens, causing atopy, allergy and asthma, have beencharacterized. The immunogenicity and manufacturing of these antigenscan likewise be improved with the methods of this invention.

The antigen library immunization methods of the invention provide ameans by which one can obtain a recombinant antigen that has improvedability to induce an immune response to a pathogenic agent. A“pathogenic agent” refers to an organism or virus that is capable ofinfecting a host cell. Pathogenic agents typically include and/or encodea molecule, usually a polypeptide, that is immunogenic in that an immuneresponse is raised against the immunogenic polypeptide. Often, theimmune response raised against an immunogenic polypeptide from oneserotype of the pathogenic agent is not capable of recognizing, and thusprotecting against, a different serotype of the pathogenic agent, orother related pathogenic agents. In other situations, the polypeptideproduced by a pathogenic agent is not produced in sufficient amounts, oris not sufficiently immunogenic, for the infected host to raise aneffective immune response against the pathogenic agent.

These problems are overcome by the methods of the invention, whichtypically involve reassembling (&/or subjecting to one or more directedevolution methods described herein) two or more forms of a nucleic acidthat encode a polypeptide of the pathogenic agent, or antigen involvedin another disease or condition. These reassembly methods, includingstochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly, use as substrates forms of thenucleic acid that differ from each other in two or more nucleotides, soa library of recombinant nucleic acids results. The library is thenscreened to identify at least one optimized recombinant nucleic acidthat encodes an optimized recombinant antigen that has improved abilityto induce an immune response to the pathogenic agent or other condition.

The resulting recombinant antigens often are chimeric in that they arerecognized by antibodies (Abs) reacting against multiple pathogenstrains, and generally can also elicit broad spectrum immune responses.Specific neutralizing antibodies are known to mediate protection againstseveral pathogens of interest, although additional mechanisms, such ascytotoxic T lymphocytes, are likely to be involved. The concept ofchimeric, multivalent antigens inducing broadly reacting antibodyresponses is further illustrated herein.

In preferred embodiments, the different forms of the nucleic acids thatencode antigenic polypeptides are obtained from members of a family ofrelated pathogenic agents.

This scheme of performing stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassemblyusing nucleic acids from different organisms is shown schematicallyherein. Therefore, these stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassemblymethods provide an effective approach to generate multivalent,crossprotective antigens. The methods are useful for obtainingindividual chimeras that effectively protect against most or allpathogen variants.

Moreover, immunizations using entire libraries or pools ofexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) antigen chimeras can alsoresult in identification of chimeric antigens that protect againstpathogen variants that were not included in the starting population ofantigens (for example, protection against strain C by experimentallyevolved (e.g. by polynucleotide reassembly &/or polynucleotidesite-saturation mutagenesis) library of chimeras/mutants of strains Aand B).

Accordingly, the antigen library immunization approach enables thedevelopment of immunogenic polypeptides that can induce immune responsesagainst poorly characterized, newly emerging pathogen variants.

Sequence reassembly (&/or one or more additional directed evolutionmethods described herein) can be achieved in many different formats andpermutations of formats, as described in further detail below. Theseformats share some common principles. For example, the targets formodification vary in different applications, as does the property soughtto be acquired or improved. Examples of candidate targets foracquisition of a property or improvement in a property include genesthat encode proteins which have immunogenic and/or toxigenic activitywhen introduced into a host organism.

The methods use at least two variant forms of a starting target. Thevariant forms of candidate substrates can show substantial sequence orsecondary structural similarity with each other, but they should alsodiffer in at least one and preferably at least two positions. Theinitial diversity between forms can be the result of natural variation,e.g., the different variant forms (homologs) are obtained from differentindividuals or strains of an organism, or constitute related sequencesfrom the same organism (e.g., allelic variations), or constitutehomologs from different organisms (interspecific variants).

Alternatively, initial diversity can be induced, e.g., the variant formscan be generated by error-prone transcription, such as an error-pronePCR or use of a polymerase which lacks proof-reading activity (see, Liao(1990) Gene 88:107-111), of the first variant form, or, by replicationof the first form in a mutator strain (mutator host cells are discussedin further detail below, and are generally well known). A mutator straincan include any mutants in any organism impaired in the functions ofmismatch repair. These include mutant gene products of mutS, mutT, mutH,mutL, ovrD, dcm, vsr, umuC, umuD, sbcB, recJ, etc. The impairment isachieved by genetic mutation, allelic replacement, selective inhibitionby an added reagent such as a small compound or an expressed antisenseRNA, or other techniques. Impairment can be of the genes noted, or ofhomologous genes in any organism. Other methods of generating initialdiversity include methods well known to those of skill in the art,including, for example, treatment of a nucleic acid with a chemical orother mutagen, through spontaneous mutation, and by inducing anerror-prone repair system (e.g., SOS) in a cell that contains thenucleic acid. The initial diversity between substrates is greatlyaugmented in subsequent steps of reassembly (&/or one or more additionaldirected evolution methods described herein) for library generation.

Properties Involved in Immunogenicity

Polynucleotide sequences that can positively or negatively affect theimmunogenicity of an antigen encoded by the polynucleotide are oftenscattered throughout the entire antigen gene. Several of these factorsare shown diagrammatically herein. By reassembling (&/or subjecting toone or more directed evolution methods described herein) different formsof polynucleotide that encode the antigen using stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly, followed by selection for those chimericpolynucleotides that encode an antigen that can induce an improvedimmune response, one can obtain primarily sequences that have a positiveinfluence on antigen immunogenicity. Those sequences that negativelyaffect antigen immunogenicity are eliminated. One need not know theparticular sequences involved.

The present invention provides methods for obtaining polynucleotidesequences that, either directly or indirectly (i.e., through encoding apolypeptide), can modulate an immune response when present on a geneticvaccine vector. In another embodiment, the invention provides methodsfor optimizing the transport and presentation of antigens. The optimizedimmunomodulatory polynucleotides obtained using the methods of theinvention are particularly suited for use in conjunction with vaccines,including genetic vaccines. One of the advantages of genetic vaccines isthat one can incorporate genes encoding immunomodulatory molecules, suchas cytokines, costimulatory molecules, and molecules that improveantigen transport and presentation into the genetic vaccine vectors.This provides opportunities to modulate immune responses that areinduced against the antigens expressed by the genetic vaccines.

Obtaining Components for Use in Genetic Vaccines that are More EffectiveThrough the Creation of a Library, the Screening of the Library, and theUse of Recombinant Nucleic Acids that Exhibit Improved Properties.

In additional embodiments, the present invention provides methods ofobtaining components for use in genetic vaccines, including themulticomponent vaccines, that are more effective in conferring a desiredimmune response property upon a genetic vaccine. The methods involvecreating a library of recombinant nucleic acids and screening thelibrary to identify those library members that exhibits an enhancedcapacity to confer a desired property upon a genetic vaccine. Thoserecombinant nucleic acids that exhibit improved properties can be usedas components in a genetic vaccine, either directly as a polynucleotideor as a protein that is obtained by expression of the component nucleicacid.

Improvement Goals

The properties or characteristics that can be sought to be acquired orimproved vary widely, and, of course depend on the choice of substrate.For genetic vaccines, improvement goals include higher titer, morestable expression, improved stability, higher specificity targeting,higher or lower frequency of integration, reduced immunogenicity of thevector or an expression product thereof, increased immunogenicity of theantigen, higher expression of gene products, and the like. Otherproperties for which optimization is desired include the tailoring of animmune response to be most effective for a particular application.Examples of genetic vaccine components are shown, described &/orreferenced herein (including incorporated by reference). Two or morecomponents can be included in a single vector molecule, or eachcomponent can be present in a genetic vaccine formulation as a separatemolecule.

Sequence Reassembly (&/or One or More Additional Directed EvolutionMethods Described Herein) can be Achieved Through Different Formatswhich Share Some Common Principles

In the methods of the invention, at least two variant forms of a nucleicacid are reassembled (&/or subjected to one or more directed evolutionmethods described herein) to produce a library of recombinant nucleicacids, which is then screened to identify at least one recombinantcomponent that is optimized for the particular vaccine property. Often,improvements are achieved after one round of reassembly (&/or one ormore additional directed evolution methods described herein) andselection. Sequence reassembly (&/or one or more additional directedevolution methods described herein) can be achieved in many differentformats and permutations of formats, as described in further detailbelow. These formats share some common principles. A family of nucleicacid molecules that have some sequence identity to each other, butdiffer in the presence of mutations, is typically used as a substratefor reassembly (&/or one or more additional directed evolution methodsdescribed herein). In any given cycle, reassembly (&/or one or moreadditional directed evolution methods described herein) can occur invivo or in vitro, intracellularly or extracellularly. Furthermore,diversity resulting from reassembly (&/or one or more additionaldirected evolution methods described herein) can be augmented in anycycle by applying prior methods of mutagenesis (e.g., error-prone PCR orcassette mutagenesis) to either the substrates or products of reassembly(&/or one or more additional directed evolution methods describedherein). In some instances, a new or improved property or characteristiccan be achieved after only a single cycle of in vivo or in vitroreassembly (&/or one or more additional directed evolution methodsdescribed herein), as when using different, variant forms of thesequence, as homologs from different individuals or strains of anorganism, or related sequences from the same organism, as allelicvariations. However, recursive sequence reassembly (&/or one or moreadditional directed evolution methods described herein), which entailssuccessive cycles of reassembly (&/or one or more additional directedevolution methods described herein), can also be employed to achievestill further improvements in a desired property, or to bring about new(or “distinct”) properties, or to generate further molecular diversity.

In a presently preferred embodiment, polynucleotides that encodeoptimized recombinant antigens are subjected to molecular backcrossing,which provides a means to breed the experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) chimeras/mutants back to a parental or wild-type sequence,while retaining the mutations that are critical to the phenotype thatprovides the optimized immune responses. In addition to removing theneutral mutations, molecular backcrossing can also be used tocharacterize which of the many mutations in an improved variantcontribute most to the improved phenotype. This cannot be accomplishedin an efficient library fashion by any other method. Backcrossing isperformed by reassembling (optionally in combination with other directedevolution methods described herein) the improved sequence with a largemolar excess of the parental sequences.

Stochastic (e.g. Polynucleotide Shuffling & Interrupted Synthesis) andNon-Stochastic Polynucleotide Reassembly is Used to Obtain the Libraryof Recombinant Nucleic Acids, Using a Variety of Substrates to Acquireor Improve Various Properties for Different Applications.

Creation of Recombinant Libraries

The invention involves creating recombinant libraries of polynucleotidesthat are then screened to identify those library members that exhibit adesired property. The recombinant libraries can be created using any ofvarious methods.

Initial Diversity Between Substrates

The substrate nucleic acids used for the reassembly (&/or one or moreadditional directed evolution methods described herein) can varydepending upon the particular application. For example, where apolynucleotide that encodes a nucleic acid binding domain or a ligandfor a cell-specific receptor is to be optimized, different forms ofnucleic acids that encode all or part of the nucleic acid binding domainor a ligand for a cell-specific receptor are subjected to reassembly(&/or one or more additional directed evolution methods describedherein).

In a presently preferred embodiment, stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly is used to obtain the library of recombinant nucleic acids.Stochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly, which is described herein, canresult in optimization of a desired property even in the absence of adetailed understanding of the mechanism by which the particular propertyis mediated. The substrates for this modification, or evolution, vary indifferent applications, as does the property sought to be acquired orimproved. Examples of candidate substrates for acquisition of a propertyor improvement in a property include viral and nonviral vectors used ingenetic vaccination, as well as nucleic acids that are involved inmediating a particular aspect of an immune response. The methods requireat least two variant forms of a starting substrate. The variant forms ofcandidate components can have substantial sequence or secondarystructural similarity with each other, but they should also differ in atleast two positions. The initial diversity between forms can be theresult of natural variation, e.g., the different variant forms(homologs) are obtained from different individuals or strains of anorganism (including geographic variants) or constitute related sequencesfrom the same organism (e.g., allelic variations). Alternatively, theinitial diversity can be induced, e.g., the second variant form can begenerated by error-prone transcription, such as an error-prone PCR oruse of a polymerase which lacks proof-reading activity (see, Liao (1990)Gene 88:107-111), of the first variant form, or, by replication of thefirst form in a mutator strain (mutator host cells are discussed infurther detail below). The initial diversity between substrates isgreatly augmented in subsequent steps of recursive sequence reassembly(&/or one or more additional directed evolution methods describedherein).

Screening or selection after a reassembly (&/or one or more additionaldirected evolution methods described herein) cycle (screening after invitro and in vivo reassembly (&/or one or more additional directedevolution methods described herein) cycles)

Once one has performed stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassembly toobtain a library of polynucleotides that encode recombinant antigens,the library is subjected to selection and/or screening to identify thoselibrary members that encode antigenic peptides that have improvedability to induce an immune response to the pathogenic agent. Selectionand screening of experimentally generated polynucleotides that encodepolypeptides having an improved ability to induce an immune response caninvolve either in vivo and in vitro methods, but most often involves acombination of these methods. For example, in a typical embodiment themembers of a library of recombinant nucleic acids are picked, eitherindividually or as pools. The clones can be subjected to analysisdirectly, or can be expressed to produce the corresponding polypeptides.In a presently preferred embodiment, an in vitro screen is performed toidentify the best candidate sequences for the in vivo studies.Alternatively, the library can be subjected to in vivo challenge studiesdirectly. The analyses can employ either the nucleic acids themselves(e.g., as genetic vaccines), or the polypeptides encoded by the nucleicacids. A schematic diagram of a typical strategy shown, described &/orreferenced herein (including incorporated by reference). Both in vitroand in vivo methods are described in more detail below.

A cycle of reassembly (&/or one or more additional directed evolutionmethods described herein) is usually followed by at least one cycle ofscreening or selection for molecules having a desired property orcharacteristic. If a cycle of reassembly (&/or one or more additionaldirected evolution methods described herein) is performed in vitro, theproducts of reassembly (&/or one or more additional directed evolutionmethods described herein), i.e., recombinant segments, are sometimesintroduced into cells before the screening step. Recombinant segmentscan also be linked to an appropriate vector or other regulatorysequences before screening.

Alternatively, products of reassembly (&/or one or more additionaldirected evolution methods described herein) generated in vitro aresometimes packaged as viruses (in viruses—e.g., bacteriophage) beforescreening. If reassembly (&/or one or more additional directed evolutionmethods described herein) is performed in vivo, product of reassembly(&/or one or more additional directed evolution methods describedherein) can sometimes be screened in the cells in which reassembly (&/orone or more additional directed evolution methods described herein)occurred. In other applications, recombinant segments are extracted fromthe cells, and optionally packaged as viruses, before screening.

Component Sequences Having Different Roles than the Product ofReassembly (&/or One or More Additional Directed Evolution MethodsDescribed Herein)

The nature of screening or selection depends on what property orcharacteristic is to be acquired or the property or characteristic forwhich improvement is sought, and many examples are discussed below. Itis not usually necessary to understand the molecular basis by whichparticular products of reassembly (&/or one or more additional directedevolution methods described herein) (recombinant segments) have acquirednew or improved properties or characteristics relative to the startingsubstrates. For example, a genetic vaccine vector can have manycomponent sequences each having a different intended role (e.g., codingsequence, regulatory sequences, targeting sequences,stability-conferring sequences, immunomodulatory sequences, sequencesaffecting antigen presentation, and sequences affecting integration).Each of these component sequences can be varied and reassembled (&/orsubjected to one or more directed evolution methods described herein)simultaneously. Screening/selection can then be performed, for example,for recombinant segments that have increased episomal maintenance in atarget cell without the need to attribute such improvement to any of theindividual component sequences of the vector.

Initial Screenings in Bacterial Cells Vs. Later Screening in MammalianCells

Depending on the particular screening protocol used for a desiredproperty, initial round(s) of screening can sometimes be performed inbacterial cells due to high transfection efficiencies and ease ofculture. However, especially for testing of immunogenic activity, testanimals are used for library expression and screening. Later rounds, andother types of screening which are not amenable to screening inbacterial cells, are generally performed (in cells selected for use inan environment close to that of their intended use) in mammalian cellsto optimize recombinant segments for use in an environment close to thatof their intended use. Final rounds of screening can be performed in thecell type of intended use (e.g., a human antigen-presenting cell). Insome instances, this cell can be obtained from a patient to be treatedwith a view, for example, to minimizing problems of immunogenicity inthis patient. In some methods, use of a genetic vaccine vector intreatment can itself be used as a round of screening. That is, geneticvaccine vectors that are successively taken up and/or expressed by theintended target cells in one patient are recovered from those targetcells and used to treat another patient. The genetic vaccine vectorsthat are recovered from the intended target cells in one patient areenriched for vectors that have evolved, i.e., have been modified byrecursive reassembly (&/or one or more additional directed evolutionmethods described herein), toward improved or new properties orcharacteristics for specific uptake, immunogenicity, stability, and thelike.

Identifying a Subpopulation of Recombinant Segments

The screening or selection step identifies a subpopulation ofrecombinant segments that have evolved toward acquisition of a new orimproved desired property or properties useful in genetic vaccination.Depending on the screen, the recombinant segments can be screened ascomponents of cells, components of viruses or other vectors, or in freeform. More than one round of screening or selection can be performedafter each round of reassembly (&/or one or more additional directedevolution methods described herein).

The Second Round of Reassembly (&/or One or More Additional DirectedEvolution Methods Described Herein)

If further improvement in a property is desired, at least one andusually a collection of recombinant segments surviving a first round ofscreening/selection are subject to a further round of reassembly (&/orone or more additional directed evolution methods described herein).These recombinant segments can be reassembled (&/or subjected to one ormore directed evolution methods described herein) with each other orwith exogenous segments representing the original substrates or furthervariants thereof. Again, reassembly (&/or one or more additionaldirected evolution methods described herein) can proceed in vitro or invivo. If the previous screening step identifies desired recombinantsegments as components of cells, the components can be subjected tofurther reassembly (&/or one or more additional directed evolutionmethods described herein) in vivo, or can be subjected to furtherreassembly (&/or one or more additional directed evolution methodsdescribed herein) in vitro, or can be isolated before performing a roundof in vitro reassembly (&/or one or more additional directed evolutionmethods described herein). Conversely, if the previous screening stepidentifies desired recombinant segments in naked form or as componentsof viruses or other vectors, these segments can be introduced into cellsto perform a round of in vivo reassembly (&/or one or more additionaldirected evolution methods described herein). The second round ofreassembly (&/or one or more additional directed evolution methodsdescribed herein), irrespective how performed, generates furtherrecombinant segments which encompass additional diversity compared torecombinant segments resulting from previous rounds.

Additional Rounds of Reassembly (&/or One or More Additional DirectedEvolution Methods Described Herein)/Screening to Sufficiently Evolve theRecombinant Segments

The second round of reassembly (&/or one or more additional directedevolution methods described herein) can be followed by a further roundof screening/selection according to the principles discussed above forthe first round. The stringency of screening/selection can be increasedbetween rounds. Also, the nature of the screen and the property beingscreened for can vary between rounds if improvement in more than oneproperty is desired or if acquiring more than one new property isdesired.

Additional rounds of reassembly (&/or one or more additional directedevolution methods described herein) and screening can then be performeduntil the recombinant segments have sufficiently evolved to acquire thedesired new or improved property or function.

The practice of this invention involves the construction of recombinantnucleic acids and the expression of genes in transfected host cells.Molecular cloning techniques to achieve these ends are known in the art.A wide variety of cloning and in vitro amplification methods suitablefor the construction of recombinant nucleic acids such as expressionvectors are well-known to persons of skill. General texts which describemolecular biological techniques useful herein, including mutagenesis,include Berger and Kimmel, Guide to Molecular Cloning Techniques,Methods in Enzymology volume 152 Academic Press, Inc., San Diego, Calif.(Berger); Sambrook et al., Molecular Cloning—A Laboratory Manual (2ndEd.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.,1989 (“Sambrook”) and Current Protocols in Molecular Biology, F. M.Ausubel et al., eds., Current Protocols, a joint venture between GreenePublishing Associates, Inc. and John Wiley & Sons, Inc., (supplementedthrough 1998) (“Ausubel”)).

Examples of techniques sufficient to direct persons of skill through invitro amplification methods, including the polymerase chain reaction(PCR) the ligase chain reaction (LCR), Q-replicase amplification andother RNA polymerase mediated techniques (e.g., NASBA) are found inBerger, Sambrook, and Ausubel, as well as Mullis et al. (1987) U.S. Pat.No. 4,683,202; PCR Protocols A Guide to Methods and Applications (Inniset al. eds) Academic Press Inc. San Diego, Calif. (1990) (Innis);Antheirn & Levinson (Oct. 1, 1990) C&EN 36-47; The Journal Of NIHResearch (1991) 3, 81-94; (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA86, 1173; Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87, 1874;Lowell et al. (1989) J Clin. Chem. 35, 1826; Landegren et al. (1988)Science 241, 1077-1080; Van Brunt (1990) Biotechnology 8, 291-294; Wuand Wallace (1989) Gene 4, 560; Barringer et al. (1990) Gene 89, 117,and Sooknanan and Malek (1995) Biotechnology 13: 563-564.

Improved methods of cloning in vitro amplified nucleic acids aredescribed in Wallace et al., U.S. Pat. No. 5,426,039. Improved methodsof amplifying large nucleic acids by PCR are summarized in Cheng et al.(1994) Nature 369: 684-685 and the references therein, in which PCRamplicons of up to 40 kb are generated. One of skill will appreciatethat essentially any RNA can be converted into a double stranded DNAsuitable for restriction digestion, PCR expansion and sequencing usingreverse transcriptase and a polymerase. See, Ausubel, Sambrook andBerger, all supra.

Oligonucleotides for use as probes, e.g., in in vitro amplificationmethods, for use as gene probes, or as reassembly targets (e.g.,synthetic genes or gene segments) are typically synthesized chemicallyaccording to the solid phase phosphoramidite triester method describedby Beaucage and Caruthers (1981) Tetrahedron Letts., 22(20):1859-1862,e.g., using an automated synthesizer, as described inNeedham-VanDevanter et al. (1984) Nucleic Acids Res., 12:6159-6168.Oligonucleotides can also be custom made and ordered from a variety ofcommercial sources known to persons of skill.

Indeed, essentially any nucleic acid with a known sequence can be customordered from any of a variety of commercial sources, such as The MidlandCertified Reagent Company (mcrc@oligos.com), The Great American GeneCompany (http://www.genco.com), ExpressGen Inc. (www.expressgen.com),Operon Technologies Inc. (Alameda, Calif.) and many others. Similarly,peptides and antibodies can be custom ordered from any of a variety ofsources, such as PeptidoGenic (pkim@ccnet.com), HTI Bio-products, Inc.(http://www.htibio.com), BMA Biomedicals Ltd (U.K.), Bio-Synthesis,Inc., and many others.

Different Formats are Available for Performing Reassembly (&/orAdditional Directed Evolution Methods Described Herein) andScreening/Selection which Allow for Large Numbers of Mutations in aMinimum Number of Selection Cycles and does not Require the ExtensiveAnalysis and Computation Required by Conventional Methods.

A number of different formats are available by which one can create alibrary of recombinant nucleic acids for screening. In some embodiments,the methods of the invention entail performing reassembly (&/or one ormore additional directed evolution methods described herein) andscreening or selection to “evolve” individual genes, whole plasmids orviruses, multigene clusters, or even whole genomes (Stemmer (1995)Bio/Technology 13:549-553). Reiterative cycles of reassembly (&/or oneor more additional directed evolution methods described herein) andscreening/selection can be performed to further evolve the nucleic acidsof interest. Such techniques do not require the extensive analysis andcomputation required by conventional methods for polypeptideengineering. Reassembly allows the combination of large numbers ofmutations in a minimum number of selection cycles, in contrast totraditional, pair wise recombination events (e.g., as occur duringsexual replication). Thus, the directed evolution techniques describedherein provide particular advantages in that they provide reassembly(optionally in combination with one or more additional directedevolution methods described herein) between any or all of the mutations,thereby providing a very fast way of exploring the manner in whichdifferent combinations of mutations can affect a desired result. In someinstances, however, structural and/or functional information isavailable which, although not required for sequence reassembly (&/or oneor more additional directed evolution methods described herein),provides opportunities for modification of the technique.

Four Different Approaches to Improve Immunogenic Activity as Well asBroaden Specificity: Reassembly (Optionally in Combination with OtherDirected Evolution Methods Described Herein) on Single Gene, SequenceComparison of Homologous Genes, Whole Genome Reassembly, CodonModification of Polypeptide-Encoding Genes.

The stochastic (e.g. polynucleotide shuffling & interrupted synthesis)and non-stochastic polynucleotide reassembly methods can involve one ormore of at least four different approaches to improve immunogenicactivity as well as to broaden specificity. First, stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly can be performed on a single gene. Secondly,several highly homologous genes can be identified by sequence comparisonwith known homologous genes. These genes can be synthesized andexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) as a family of homologs, toselect recombinants with the desired activity. The experimentallyevolved (e.g. by polynucleotide reassembly &/or polynucleotidesite-saturation mutagenesis) genes can be introduced into appropriatehost cells, which can include E. coli, yeast, plants, fungi, animalcells, and the like, and those having the desired properties can beidentified by the methods described herein. Third, whole genomereassembly can be performed to shuffle genes that can confer a desiredproperty upon a genetic vaccine (along with other genomic nucleicacids). For whole genome reassembly approaches, it is not even necessaryto identify which genes are being experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis). Instead, e.g., bacterial cell or viral genomes arecombined and experimentally evolved (e.g. by polynucleotide reassembly&/or polynucleotide site-saturation mutagenesis) to acquire recombinantnucleic acids that, either itself or through encoding a polypeptide,have enhanced ability to induce an immune response, as measured in anyof the assays described herein. Fourth, polypeptide-encoding genes canbe codon modified to access mutational diversity not present in anynaturally occurring gene.

References for Formats and Examples for Sequence Reassembly (&/or One orMore Additional Directed Evolution Methods Described Herein) and forOther Methods

Exemplary formats and examples for polynucleotide reassembly, gene sitesaturation mutagenesis, interrupted synthesis, and additional directedevolution methods described herein have been described by the presentinventors and co-workers in issued and co-pending applications includingU.S. Pat. No. 5,965,408 (issued Oct. 12, 1999), U.S. Pat. No. 5,830,696(issued Nov. 3, 1998), and U.S. Pat. No. 5,939,250 (issued Aug. 17,1999).

Other methods for obtaining libraries of experimentally generatedpolynucleotides and/or for obtaining diversity in nucleic acids used asthe substrates for directed evolution including stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly include, for example, WO98/42727; Smith, Ann.Rev. Genet. 19: 423-462 (1985); Botstein and Shortle, Science 229:1193-1201 (1985); Carter, Biochem. J 237: 1-7 (1986); Kunkel, “Theefficiency of oligonucleotide directed mutagenesis” in Nucleic acids &Molecular Biology, Eckstein and Lilley, eds., Springer Verlag, Berlin(1987)). Included among these methods are oligonucleotide-directedmutagenesis (Zoller and Smith, Nucl. Acids Res. 10: 6487-6500 (1982),Methods in Enzymol. 100: 468-500 (1983), and Methods in Enzymol. 154:329-350 (1987)) phosphothioate-modified DNA mutagenesis (Taylor et al.,Nucl. Acids Res. 13: 8749-8764 (1985); Taylor et al., Nucl. Acids Res.13: 8765-8787 (1985); Nakamaye and Eckstein, Nucl. Acids Res. 14:9679-9698 (1986); Sayers et al., Nucl. Acids Res. 16: 791-802 (1988);Sayers et al., Nucl. Acids Res. 16: 803-814 (1988)), mutagenesis usinguracil-containing templates (Kunkel, Proc. Nat'l. Acad. Sci. USA 82:488-492 (1985) and Kunkel et al., Methods in Enzymol. 154: 367-382));mutagenesis using gapped duplex DNA (Kramer et al., Nucl. Acids Res. 12:9441-9456 (1984); Kramer and Fritz, Methods in Enzymol. 154: 350-367(1987); Kramer et al., Nucl. Acids Res. 16: 7207 (1988)); and Fritz etal., Nucl. Acids Res. 16: 6987-6999 (1988)). Additional suitable methodsinclude point mismatch repair (Kramer et al., Cell 38: 879-887 (1984)),mutagenesis using repair-deficient host strains (Carter et al., Nucl.Acids Res. 13: 4431-4443 (1985); Carter, Methods in Enzymol. 154:382-403 (1987)), deletion mutagenesis (Eghtedarzadeh and Henikoff, Nucl.Acids Res. 14: 5115 (1986)), restriction-selection andrestriction-purification (Wells et al., Phil. Trans. R. Soc. Lond. A317: 415-423 (1986)), mutagenesis by total gene synthesis (Nambiar etal., Science 223: 1299-1301 (1984); Sakamar and Khorana, Nucl. AcidsRes. 14: 6361-6372 (1988); Wells et al., Gene 34: 315-323 (1985); andGrundstrom et al., Nucl. Acids Res. 13: 3305-3316 (1985). Kits formutagenesis are commercially available (e.g., Bio-Rad, AmershamInternational, Anglian Biotechnology).

For Reassembly (&/or One or More Additional Directed Evolution MethodsDescribed Herein) to Generate Increased Diversity Relative to theStarting Materials, the Starting Materials Must Differ from Each Otherin at Least Two Nucleotide Positions.

The reassembly procedure starts with at least two substrates thatgenerally show substantial sequence identity to each other (i.e., atleast about 30%, 50%, 70%, 80% or 90% sequence identity), but differfrom each other at certain positions. The difference can be any type ofmutation, for example, substitutions, insertions and deletions. Often,different segments differ from each other in about 5-20 positions. Forreassembly (&/or one or more additional directed evolution methodsdescribed herein) to generate increased diversity relative to thestarting materials, the starting materials must differ from each otherin at least two nucleotide positions. That is, if there are only twosubstrates, there should be at least two divergent positions. If thereare three substrates, for example, one substrate can differ from thesecond at a single position, and the second can differ from the third ata different single position. The starting DNA segments can be naturalvariants of each other, for example, allelic or species variants. Thesegments can also be from nonallelic genes showing some degree ofstructural and usually functional relatedness (e.g., different geneswithin a superfamily, such as the family of Yersinia V− antigens, forexample). The starting DNA segments can also be induced variants of eachother. For example, one DNA segment can be produced by error-prone PCRreplication of the other, the nucleic acid can be treated with achemical or other mutagen, or by substitution of a mutagenic cassette.Induced mutants can also be prepared by propagating one (or both) of thesegments in a mutagenic strain, or by inducing an error-prone repairsystem in the cells.

The Different Segments Forming the Starting Materials are Related, andMight or Might not be of Similar Length

In these situations, strictly speaking, the second DNA segment is not asingle segment but a large family of related segments. The differentsegments forming the starting materials are often the same length orsubstantially the same length. However, this need not be the case; forexample; one segment can be a subsequence of another. The segments canbe present as part of larger molecules, such as vectors, or can be inisolated form.

The Starting DNA Segments are Reassembled (&/or Subjected to One or MoreDirected Evolution Methods Described Herein) to Generate a Library ofRecombinant DNA Segments Varying in Size which Will Include Full LengthCoding Sequences and Any Essential Regulatory

The starting DNA segments are reassembled (&/or subjected to one or moredirected evolution methods described herein) by any of the sequencereassembly (&/or one or more additional directed evolution methodsdescribed herein) formats provided herein to generate a diverse libraryof recombinant DNA segments. Such a library can vary widely in size fromhaving fewer than 10 to more than 10⁵, 10⁹, 10¹² or more members. Insome embodiments, the starting segments and the recombinant librariesgenerated will include full-length coding sequences and any essentialregulatory sequences, such as a promoter and polyadenylation sequence,required for expression. In other embodiments, the recombinant DNAsegments in the library can be inserted into a common vector providingsequences necessary for expression before performingscreening/selection.

Using Reassembly PCR to Assemble Multiple Segments that have beenSeparately Evolved into a Full Length Nucleic Acid Template such as aGene

A further technique for recombining mutations in a nucleic acid sequenceutilizes “reassembly PCR”. This method can be used to assemble multiplesegments that have been separately evolved into a full length nucleicacid template such as a gene. This technique is performed when a pool ofadvantageous mutants is known from previous work or has been identifiedby screening mutants that may have been created by any mutagenesistechnique known in the art, such as PCR mutagenesis, cassettemutagenesis, doped oligo mutagenesis, chemical mutagenesis, orpropagation of the DNA template in vivo in mutator strains. Boundariesdefining segments of a nucleic acid sequence of interest preferably liein intergenic regions, introns, or areas of a gene not likely to havemutations of interest.

Oligos are Synthesized for PCR Amplification of Segments of the NucleicAcid Sequence of Interest so that the Oligos Overlap the Junctions ofTwo Segments by, Typically, About 10 to 100 Nucleotides

Preferably, oligonucleotide primers (oligos) are synthesized for PCRamplification of segments of the nucleic acid sequence of interest, suchthat the sequences of the oligonucleotides overlap the junctions of twosegments. The overlap region is typically about 10 to 100 nucleotides inlength. Each of the segments is amplified with a set of such primers.The PCR products are then “reassembled” according to assembly protocolssuch as those discussed herein to assemble non-stochastically generatednucleic acid building blocks &/or randomly fragmented genes. In brief,in an assembly protocol the PCR products are first purified away fromthe primers, by, for example, gel electrophoresis or size exclusionchromatography. Purified products are mixed together and subjected toabout 1-10 cycles of denaturing, reannealing, and extension in thepresence of polymerase and deoxynucleoside triphosphates (dNTP's) andappropriate buffer salts in the absence of additional primers(“self-priming”). Subsequent PCR with primers flanking the gene are usedto amplify the yield of the fully reassembled and experimentally evolved(e.g. by polynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) genes.

PCR Primers are Used to Introduce Variation into the Gene of Interestand the Mutations at Sites of Interest are Screened or Selected bySequencing Homologues of the Nucleic Acid Sequence

In a further embodiment, PCR primers for amplification of segments ofthe nucleic acid sequence of interest are used to introduce variationinto the gene of interest as follows. Mutations at sites of interest ina nucleic acid sequence are identified by screening or selection, bysequencing homologues of the nucleic acid sequence, and so on.

Using Oligonucleotide PCR Primers (Encoding Wild Type or MutantInformation) in PCR to Generate Libraries of Full Length Genes EncodingPermutations of Said Info, where the Alternative Screening or SelectionProcess is Expensive, Cumbersome, or Impractical

Oligonucleotide PCR primers are then synthesized which encode wild typeor mutant information at sites of interest. These primers are then usedin PCR mutagenesis to generate libraries of full length genes encodingpermutations of wild type and mutant information at the designatedpositions. This technique is typically advantageous in cases where thescreening or selection process is expensive, cumbersome, or impracticalrelative to the cost of sequencing the genes of mutants of interest andsynthesizing mutagenic oligonucleotides.

2.3. Vectors Used in Genetic Vaccination

Evolution of Genetic Vaccines and Components by Stochastic (e.g.Polynucleotide Shuffling & Interrupted Synthesis) and Non-StochasticPolynucleotide Reassembly

The invention provides multicomponent genetic vaccines, and methods ofobtaining genetic vaccine components that improve the capability of thegenetic vaccine for use in nucleic acid-mediated immunomodulation. Ageneral approach for evolution of genetic vaccines and components bystochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly is shown schematically herein.

Including an Origin of Replication is Useful to Obtain SufficientQuantities of the Vector Prior to Administration to a Patient, but Mightbe Undesirable if the Vector is Designed to Integrate into HostChromosomal DNA or Bind to Host mRNA or DNA.

Broadly speaking, a genetic vaccine vector is an exogenouspolynucleotide which produces a medically useful phenotypic effect uponthe mammalian cell(s) and organisms into which it is transferred. Avector may or may not have an origin of replication. For example, it isuseful to include an origin of replication in a vector to allow forpropagation of the vector in order to obtain sufficient quantities ofthe vector prior to administration to a patient. If the vector isdesigned to integrate into host chromosomal DNA or bind to host mRNA orDNA, or if replication in the host is otherwise undesirable, the originof replication can be removed before administration, or an origin can beused that functions in the cells used for vector production but not inthe target cells. However, in certain situations, including some ofthose discussed herein, it is desirable that the genetic vaccine vectorbe capable of replicating in appropriate host cells.

Incorporating Nucleic Acids that are Modified by Stochastic (e.g.Polynucleotide Shuffling & Interrupted Synthesis) and Non-StochasticPolynucleotide Reassembly into Viral Vectors to be Used in GeneticVaccination

Vectors used in genetic vaccination can be viral or nonviral. Viralvectors are usually introduced into a patient as components of a virus.Illustrative viral vectors into which one can incorporate nucleic acidsthat are modified by the stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassemblymethods of the invention include, for example, adenovirus-based vectors(Cantwell (1996) Blood 88:4676-4683; Ohashi (1997) Proc. Nat'l. Acad.Sci. USA 94:1287-1292), Epstein-Barr virus-based vectors (Mazda (1997)J. Immunol. Methods 204:143-151), adenovirus-associated virus vectors,Sindbis virus vectors (Strong (1997) Gene Ther. 4: 624-627), herpessimplex virus vectors (Kennedy (1997) Brain 120: 1245-1259) andretroviral vectors (Schubert (1997) Curr. Eye Res. 16:656-662).

Techniques for Transferring DNA into a Cell Useful In Vivo (Naked DNADelivered Using Liposomes Fusing to Cellular Membrane or EnteringThrough Endocytosis; Permeabilize the Cells and Use DNA Binding Proteinto Transport into Cell; and Bombardment of Skin with Particles Coatedwith DNA Delivered Mechanically)

Nonviral vectors, typically dsDNA, can be transferred as naked DNA orassociated with a transfer-enhancing vehicle, such as areceptor-recognition protein, liposome, lipoamine, or cationic lipid.This DNA can be transferred into a cell using a variety of techniqueswell known in the art. For example, naked DNA can be delivered by theuse of liposomes which fuse with the cellular membrane or areendocytosed, i.e., by employing ligands attached to the liposome, orattached directly to the DNA, that bind to surface membrane proteinreceptors of the cell resulting in endocytosis. Alternatively, the cellsmay be permeabilized to enhance transport of the DNA into the cell,without injuring the host cells. One can use a DNA binding protein,e.g., HBGF-1, known to transport DNA into a cell. Furthermore, DNA canbe delivered by bombardment of the skin by gold or other particlescoated with DNA which are delivered by mechanical means, e.g., pressure.These procedures for delivering naked DNA to cells are useful in vivo.For example, by using liposomes, particularly where the liposome surfacecarries ligands specific for target cells, or are otherwisepreferentially directed to a specific organ, one may provide for theintroduction of the DNA into the target cells/organs in vivo.

2.3.1. Viral Vectors

Structure of Viral Vectors Often Consist of a Modified Viral Genome anda Coat Structure Surrounding it, a Structure which can be Changed inMany Ways for the Viral Nucleic Acid in a Vector Designed for GeneticVaccination.

Various viral vectors, such as retroviruses, adenoviruses,adenoassociated viruses and herpes viruses, are commonly used in geneticvaccination. They are often made up of two components, a modified viralgenome and a coat structure surrounding it (see generally Smith (1995)Annu. Rev. Microbiol. 49, 807-838), although sometimes viral vectors areintroduced in naked form or coated with proteins other than viralproteins. Most current viral vectors have coat structures similar to awild type virus. This structure packages and protects the viral nucleicacid and provides the means to bind and enter target cells. In contrast,the viral nucleic acid in a vector designed for genetic vaccination canbe changed in many ways. The goals of these changes can be, for example,to enhance or reduce replication of the virus in target cells whilemaintaining its ability to grow in vector form in available packaging orhelper cells, to incorporate new sequences that encode and enableappropriate expression of a gene of interest (e.g., an antigen-encodinggene), and to alter the immunogenicity of the viral vector itself. Viralvector nucleic acids generally comprise two components: essentialcis-acting viral sequences for replication and packaging in a helperline and a transcription unit for the exogenous gene. Other viralfunctions can be expressed in trans in a specific packaging or helpercell line.

2.3.1.1. Adenoviruses

The Normal Life Cycle and Production Infection Cycle of Adenoviruses.

Adenoviruses comprise a large class of nonenveloped viruses that containlinear double-stranded DNA. The normal life cycle of the virus does notrequire dividing cells and involves productive infection in permissivecells during which large amounts of virus accumulate. The productiveinfection cycle takes about 32-36 hours in cell culture and comprisestwo phases, the early phase, prior to viral DNA synthesis, and the latephase, during which structural proteins and viral DNA are synthesizedand assembled into virions.

In general, adenovirus infections are associated with mild disease inhumans.

E3-Deletion Vectors Studied; Replication in Cultured Cells does notRequire E3 Region, Allowing Insertion of Exogenous DNA Sequences toYield Vectors Capable of Productive Infection and the TransientSynthesis of Relatively Large Amounts of Encoded Protein.

Adenovirus vectors are somewhat larger and more complex than retrovirusor AAV vectors, partly because only a small fraction of the viral genomeis removed from most current vectors. If additional genes are removed,they are provided in trans to produce the vector, which so far hasproved difficult. Instead, two general types of adenovirus-based vectorshave been studied, E3-deletion and E1-deletion vectors. Some viruses inlaboratory stocks of wild-type lack the E3 region and can grow in theabsence of helper. This ability does not mean that the E3 gene productsare not necessary in the wild, only that replication in cultured cellsdoes not require them. Deletion of the E3 region allows insertion ofexogenous DNA sequences to yield vectors capable of productive infectionand the transient synthesis of relatively large amounts of encodedprotein.

E1 Replacement Vectors Grown in 293 Cells Utilized in Most Gene TherapyApplications Involving Adenoviruses.

Deletion of the E1 region disables the adenovirus, but such vectors canstill be grown because there exists an established human cell line(called “293”) that contains the E1 region of Ad5 and thatconstitutively expresses the E1 proteins. Most recent gene-therapyapplications involving adenovirus have utilized E1 replacement vectorsgrown in 293 cells.

Adenovirus Vectors Capable of Efficient Episomal Gene Transfer, Easy toGrow, can be Topically Applied to Skin for Antigen Delivery, Inductionof Antigen Specific Immune Responses can be Observed, but Host ResponseLimits Duration of Expression and Ability to Repeat Dosing in Cases withHigh Doses of First Generation Vectors

The main advantages of adenovirus vectors are that they are capable ofefficient episomal gene transfer in a wide range of cells and tissuesand that they are easy to grow in large amounts. Adenovirus-basedvectors can also be used to deliver antigens after topical applicationonto the skin, and induction of antigen-specific immune responses can beobserved following delivery to the skin (Tang et al. (1997) Nature 388:729-730). The main disadvantage is that the host response to the virusappears to limit the duration of expression and the ability to repeatdosing, at least with high doses of first-generation vectors.

This Invention Provides for the First Time a Phagemid System Capable ofCloning Large DNA Inserts of Over 10 Kilobases and Generating ssDNA InVitro and In Vivo Corresponding to Those Large Inserts.

In one embodiment, the directed evolution methods of the invention areused to construct a novel adenovirus-phagemid capable of packaging DNAinserts over 10 kilobases in size. Incorporation of a phage origin in aplasmid using the methods of the invention also generates a novel invivo reassembly or shuffling format capable of evolving whole genomes ofviruses, such as the 36 kb family of human adenoviruses. The widely usedhuman adenovirus type 5 (Ad5) has a genome size of 36 kb. It isdifficult to shuffle this large genome in vitro without creating anexcessive number of changes which may cause a high percentage ofnonviable recombinant variants. To minimize this problem and achievewhole genome reassembly of Ad5, an adenovirus-phagemid was constructed.The Ad-phagemid has been demonstrated to accept inserts as large as 15and 24 kilobases and to effectively generate ssDNA of that size. In afurther embodiment, larger DNA inserts, as large as 50 to 100 kb areinserted into the Ad-phagemid of the invention; with generation of fulllength ssDNA corresponding to those large inserts. Generation of suchlarge ssDNA non-stochastically generated nucleic acid building blocks&/or fragments provides a means to evolve, i.e. modify by the recursivereassembly methods (&/or one or more additional recursive directedevolution methods described herein) of the invention, entire viralgenomes. Thus, this invention provides for the first time a uniquephagemid system capable of cloning large DNA inserts (>10 KB) andgenerating ssDNA in vitro and in vivo corresponding to those largeinserts.

In Vivo Reassembly or Shuffling of the Genomes of Related Serotypes ofHuman Adenoviruses Using System is Useful for Creation of RecombinantAdenovirus Variants with Changes in Multiple Genes.

The genomes of related serotypes of human adenovirus are experimentallyevolved (e.g. by polynucleotide reassembly &/or polynucleotidesite-saturation mutagenesis) in vivo using this unique phagemid system,as described in International Application No. PCT/US97/17302 (Publ. No.WO98/13485). The genomic DNA is first cloned into a phagemid vector, andthe resulting plasmid, designated an “Admid,” can be used to producesingle-stranded (ss) Admid phage by using a helper M13 phage. To achievein vivo reassembly (&/or one or more additional directed evolutionmethods described herein), ssAdmid phages containing the genome ofhomologous human adenoviruses are used to perform high multiplicity ofinfection (MOI) on F⁺ MutS E. coli cells. The ssDNA is a bettersubstrate for reassembly (&/or one or more additional directed evolutionmethods described herein) enzymes such as RecA. The high MOI ensuresthat the probability of having multiple cross-overs between copies ofthe infecting ssAdmid DNA is high. The experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) adenovirus genome is generated by purification of thedouble stranded Admid DNA from the infected cells and is introductioninto a permissive human cell line to produce the adenovirus library.This genomic reassembly strategy is useful for creation of recombinantadenovirus variants with changes in multiple genes. This allowsscreening or selection of recombinant variant phenotypes resulting fromcombinations of variations in multiple genes.

2.3.1.2. Adeno-Associated Virus (AAV)

AAV is a small, simple, nonautonomous virus containing linearsingle-stranded DNA. See, Muzycka, Current Topics Microbiol. Immunol.158, 97-129 (1992). The virus requires co-infection with adenovirus orcertain other viruses in order to replicate. AAV is widespread in thehuman population, as evidenced by antibodies to the virus, but it is notassociated with any known disease. AAV genome organization isstraightforward, comprising only two genes: rep and cap. The termini ofthe genome comprises terminal repeats (ITR) sequences of about 145nucleotides.

Growth of AAV is Cumbersome and Helper Virus Such as Adenovirus is OftenRequired.

AAV-based vectors typically contain only the ITR sequences flanking thetranscription unit of interest. The length of the vector DNA cannotgreatly exceed the viral genome length of 4680 nucleotides. Currently,growth of AAV vectors is cumbersome and involves introducing into thehost cell not only the vector itself but also a plasmid encoding rep andcap to provide helper functions. The helper plasmid lacks ITRs andconsequently cannot replicate and package. In addition, helper virussuch as adenovirus is often required.

Advantage: Long-Term Expression in Nondividing Cells.

The potential advantage of AAV vectors is that they appear capable oflong-term expression in nondividing cells, possibly, though notnecessarily, because the viral DNA integrates. The vectors arestructurally simple, and they may therefore provoke less of a host-cellresponse than adenovirus.

2.3.1.3. Papilloma Virus

Papillomaviruses are small, nonenveloped, icosahedral DNA viruses thatreplicate in the nucleus of squamous epithelial cells. Papillomavirusesconsist of a single molecule of double-stranded circular DNA about 8,000bp in size within a spherical protein coat of 72 capsomeres. Suchpapillomaviruses are classified by the species they infect (e.g.,bovine, human, rabbit) and by type within species. Over 50 distincthuman papillomaviruses (“HPV”) have been described. See, e.g., FieldsVirology (3rd ed., eds. Fields et al., Lippincott-Raven, Philadelphia,1996).

Cellular Tropism for Epithelial Cells

Papillomaviruses display a marked degree of cellular tropism forepithelial cells. Specific viral types have a preference for eithercutaneous or mucosal epithelial cells.

Benign, Low-Risk, Intermediate-Risk, and High-Risk HPVs.

All papillomaviruses have the capacity to induce cellular proliferation.The most common clinical manifestation of proliferation is theproduction of benign warts. However, many papillomaviruses have capacityto be oncogenic in some individuals and some papillomaviruses are highlyoncogenic. Based on the pathology of the associated lesions, most humanpapillomaviruses (HPVs) can be classified in one of four major groups,benign, low-risk, intermediate-risk and high-risk (Fields Virology,(Fields et al., eds., Lippincott-Raven, Philadelphia, 3d ed. 1996); DNATumor Viruses: Papilloma in (Encyclopedia of Cancer, Academic Press)Vol. 1, p 520-531). For example, viruses HPV-1, HPV-2, HPV-3, HPV-4, andHPV-27 are associated with benign cutaneous lesions. Viruses HPV-6 andHPV-11 are associated with vulval, penile, and laryngeal warts and areconsidered low-risk viruses as they are rarely associated with invasivecarcinomas. Viruses HPV-16, HPV-18, HPV-31, and HPV-45 are consideredhigh risk virus as they are associated with a high frequency with adeno-and squamous carcinoma of the cervix. Viruses HPV-5 and HPV-8 areassociated with benign cutaneous lesion in a multifactorial diseaseEpidermodysplasia Verruciformis (EV). Such lesions, however, canprogress into squamous cell carcinomas.

HPVs Classified for Risk Based on Frequency of Cancerous LesionsRelative to Previously Classified HPVs.

These viruses do not fall under one of the four major risk groups. Newlydiscovered HPVs can classified for risk based on the frequency ofcancerous lesions relative to that of HPVs that have already beenclassified for risk.

HPV vectors can be subjected to iterative cycles of reassembly (&/or oneor more additional directed evolution methods described herein) andscreening with a view to obtaining vectors with improved properties.Improved properties include increased tissue specificity, altered tissuespecificity, increased expression level, prolonged expression, increasedepisomal copy number, increased or decreased capacity for chromosomalintegration, increased uptake capacity, and other properties asdiscussed herein. The starting materials for reassembling (optionally incombination with other directed evolution methods described herein) aretypically vectors of the kind described above constructed from differentstrains of human papillomaviruses, or segments or variants of suchgenerated by e.g., error-prone PCR or cassette mutagenesis. The humanpapillomaviruses, or at least the E1 and E2 coding regions thereof arepreferably human cutaneous papillomaviruses.

2.3.1.4. Retroviruses

Normal Viral Life Cycle and Viral Genome Organization.

Retroviruses comprise a large class of enveloped viruses that containsingle-stranded RNA as the viral genome. During the normal viral lifecycle, viral RNA is reverse-transcribed to yield double-stranded DNAthat integrates into the host genome and is expressed over extendedperiods. As a result, infected cells shed virus continuously withoutapparent harm to the host cell. The viral genome is small (approximately10 kb), and its prototypical organization is extremely simple,comprising three genes encoding gag, the group specific antigens or coreproteins; pol, the reverse transcriptase; and env, the viral envelopeprotein. The termini of the RNA genome are called long terminal repeats(LTRs) and include promoter and enhancer activities and sequencesinvolved in integration. The genome also includes a sequence requiredfor packaging viral RNA and splice acceptor and donor sites forgeneration of the separate envelope mRNA. Most retroviruses canintegrate only into replicating cells, although human immunodeficiencyvirus (HIV) appears to be an exception.

Providing the Missing Viral Functions to the Retrovirus Vector andAdding/Removing Additional Features to Render the Vectors MoreEfficacious or Reduce the Possibility of Contamination by Helper Virus.

Retrovirus vectors are relatively simple, containing the 5′ and 3′ LTRs,a packaging sequence, and a transcription unit composed of the gene orgenes of interest, which is typically an expression cassette. To growsuch a vector, one must provide the missing viral functions in transusing a so-called packaging cell line. Such a cell is engineered tocontain integrated copies of gag, pol, and env but to lack a packagingsignal so that no helper virus sequences become encapsidated. Additionalfeatures added to or removed from the vector and packaging cell linereflect attempts to render the vectors more efficacious or reduce thepossibility of contamination by helper virus.

Potentially Capable of Long-Term Expression, can be Grown in LargeAmounts, but Must Ensure the Absence of Helper Virus.

For some genetic vaccine applications, retroviral vectors have theadvantage of being able to integrate in the chromosome and thereforepotentially capable of long-term expression. They can be grown inrelatively large amounts, but care is needed to ensure the absence ofhelper virus.

2.3.2. Non-Viral Genetic Vaccine Vectors

Nonviral nucleic acid vectors used in genetic vaccination includeplasmids, RNAs, polyamide nucleic acids, and yeast artificialchromosomes (YACs), and the like.

Vector Organization; Insertion of Enhancer Sequence IncreasesTranscription.

Such vectors typically include an expression cassette for expressing apolypeptide against which an immune response is induced. The promoter insuch an expression cassette can be constitutive, cell type-specific,stage-specific, and/or modulatable (e.g., by tetracycline ingestion;tetracycline-responsive promoter). Transcription can be increased byinserting an enhancer sequence into the vector. Enhancers are cis-actingsequences, typically between 10 to 300 base pairs in length, thatincrease transcription by a promoter. Enhancers can effectively increasetranscription when either 5′ or 3′ to the transcription unit. They arealso effective if located within an intron or within the coding sequenceitself. Typically, viral enhancers are used, including SV40 enhancers,cytomegalovirus enhancers, polyoma enhancers, and adenovirus enhancers.Enhancer sequences from mammalian systems are also commonly used, suchas the mouse immunoglobulin heavy chain enhancer.

Methods for Introduction of Nonviral Vectors into an Animal.

Nonviral vectors encoding products useful in gene therapy can beintroduced into an animal by means such as lipofection, biolistics,virosomes, liposomes, immunoliposomes, polycation:nucleic acidconjugates, naked DNA injection, artificial virions, agent-enhanceduptake of DNA, ex vivo transduction. Lipofection is described in e.g.,U.S. Pat. Nos. 5,049,386, 4,946,787; and 4,897,355) and lipofectionreagents are sold commercially (e.g., Transfectam™ and Lipofectin™).Cationic and neutral lipids that are suitable for efficientreceptor-recognition lipofection of polynucleotides include those ofFelgner, WO 91/17424, WO 91/16024. Naked DNA genetic vaccines aredescribed in, for example, U.S. Pat. No. 5,589,486.

2.4. Multicomponent Genetic Vaccines Use of Two or More Separate GeneticVaccine Components for Immunization, Providing a Means for ElicitingDifferentiated Responses in Different Cell Types.

The invention provides multicomponent genetic vaccines that are designedto obtain an optimal immune response upon administration to a mammal. Inthese vaccines, two or more separate genetic vaccine components are usedfor immunization, preferably in the same formulation. Each component canbe optimized for particular functions that will occur in some cells andnot in others, thus providing a means for eliciting differentiatedresponses in different cell types. When mutually incompatibleconsequences are derived from use of one plasmid, those activities areseparated into different vectors that will have different fates andeffects in vivo. Genetic vaccines are ideal for the formulation ofseveral biologically active entities into one preparation. The vectorsare preferably all of the same chemical type so there is noincompatibility of this nature, and can all be manufactured by the samechemical and/or biological processes. The vaccine preparation canconsist of a defined molar ratio of the separate vector components thatcan be formulated exactly and repeatedly.

Developing Vector Components without Knowledge of Mechanism by which aParticular Feature is Controlled or Property to be Modified

Several genetic vaccine vector components that can be used as componentsof a multicomponent genetic vaccine are described below. The methods ofthe invention greatly simplify the development of such vectorcomponents, because the mechanism by which a particular feature iscontrolled and the properties of a molecule that, when modified, willenhance that feature, need not be known. Even in the absence of suchknowledge, by carrying out the reassembly (&/or one or more additionaldirected evolution methods described herein) and screening methods ofthe invention, one can obtain vector components that are improved foreach of the properties listed.

2.4. Vector “AR”, Designed to Provide Optimal Antigen Release

Genetic vaccine vector component “AR” is designed to provide optimalrelease of antigen in a form that will be recognized by antigenpresenting cells (APC) and taken up by those cells for efficientintracellular processing and presentation to T helper (T_(H)) cells.Cells transfected with AR plasmid can be considered as an antigenfactory for APC.

AR plasmids typically have one or more of the following properties, eachof which can be optimized using the stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly methods of the invention.

(a) Optimal Plasmid Binding to and Uptake by the Chosen AntigenExpressing Cells (e.g., Myocytes for Intramuscular Immunization orEpithelial Cells for Mucosal Immunization)

This is a critical property which differentiates AR from other vectorcomponents in the multicomponent DNA vaccine. Optimal vector binding tothe target cell includes not only the concept of very avid binding andsubsequent internalization into target cells, but relative inability tobind to and enter other cells. Optimization of this ratio of desiredbinding to undesired binding will significantly increase the number oftarget cells transfected. This property can be optimized usingstochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly according to the presentinvention as described herein. For example, variant vector componentsequences obtained by stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassembly,combinatorial assembly of vector components, insertion of randomoligonucleotide sequences, and the like, can first be selected for thosethat bind to target cells, after which this population of cells isdepleted for those that bind to other cells. Vector components fortargeting genetic vaccine vectors to particular cell types, and methodsof obtaining improved targeting, are described in

(b) Optimal Trafficking of the Vector DNA to the Nucleus.

Again, the present invention provides methods by which one can obtaingenetic vaccine components that are optimal for such properties.

(c) Optimal Transcription of the Antigen Gene(s).

This can involve, for example, the use of optimized promoters,enhancers, introns, and the like. In a preferred embodiment,cell-specific promoters are used that only allow transcription of thegenes when the vector is within the nucleus of the target cell type. Inthis case, specificity is derived not only from selective vector entryinto target cells.

(d) Optimal Trafficking of mRNA to the Cytoplasm and Optimal Longevityof the mRNA in the Cytoplasm.

To achieve this property, the methods of the invention are used toobtain optimal 3′ and 5′ non-translated regions of the mRNA.

(e) Optimal Translation of the mRNA.

Again, the stochastic (e.g. polynucleotide shuffling & interruptedsynthesis) and non-stochastic polynucleotide reassembly methods are usedto obtain optimized recombinant sequences which exhibit optimal ribosomebinding and assembly of translational machinery, plus optimal codonpreference.

(f) Optimal Antigen Structure for Efficient Uptake by APC.

Extracellular antigen is taken up by APC by at least five non-exclusivemechanisms. One mechanism is sampling of the external fluid phase bymicropinocytosis and internalization of a vesicle.

Additional Mechanistic Considerations

The first mechanism has, as far as is presently known, no structuralrequirements for an antigen in the fluid phase and is therefore notrelevant to considerations of designing antigen structure. A secondmechanism involves binding of antigen to receptors on the APC surface;such binding occurs according to rules that are only now being studied(these receptors are not immunoglobulin family members and appear torepresent several families of proteins and glycoproteins capable ofbinding different classes of extracellular proteins/glycoproteins). Thistype of binding is followed by receptor-mediated internalization, alsoin a vesicle. Because this mechanism is poorly understood at present,elements of antigen design cannot be incorporated in a rational designprocess. However, application of stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly methods, an empirical approach of selection of variant DNAmolecules most successful at entry into APC, can select for variantsthat are improved throughout this mechanism.

The other three mechanisms all relate to specific antibody recognitionof the extracellular antigen. The first mechanism involvesimmunoglobulin-mediated recognition of the specific antigen via IgG thatis bound to Fc receptors on the cell surface. APC such as monocytes,macrophages and dendritic cells can be decorated with surface membraneIgG of diverse specificities. In a primary response, this mechanism willnot be operative. In previously immunized animals, IgG on the surface ofAPC can specifically bind extracellular antigen and mediate uptake ofthe bound antigen into an intracellular endosomal compartment. Anothermechanism involves binding to clonally-derived surface membraneimmunoglobulin which is present on each B cells (IgM in the case ofprimary B cells and IgG when the animal has been previously exposed tothe antigen). B cells are efficient APC. Extracellular antigen can bindspecifically to surface Ig and be internalized and processed in amembrane compartment for presentation on the B cell surface. Finally,extracellular antigen can be recognized by specific solubleimmunoglobulin (IgM in the case of a primary immunization and IgG in thepreviously immunized animals). Complexing with Ig will elicit binding tothe surface of APC (via Fc receptor recognition in the case of IgG) andinternalization.

In each of these latter three mechanisms, the extent to which theconformation of the antigen is the same as the recognition specificityof the pre-existing antibody is critical to the efficiency of theprocess of antigen presentation. Antibodies can recognize linear proteinepitopes as well as conformational epitopes determined by the threedimensional structure of the protein antigen. Protective antibodies thatwill recognize an extracellular virus or bacterial pathogen and bybinding to its surface prevent infection or mediate its immunedestruction (complement mediated lysis, immune complex formation andphagocytosis) are almost exclusively generated against conformationaldeterminants on the proteins with native structure displayed on thesurface of the pathogen. Hence, it is imperative for generation of hostprotective humoral immunity, to have those naive B cells which bearantibody specific for conformational epitopes present on the pathogen bestimulated by direct contact with T helper cells after intracellularprocessing of the antigen and presentation of degradation peptides inthe context of MHC Class II. This T help will allow selectiveproliferation of the relevant B cells with consequent mutation ofantibody and antigen driven selection for antibodies with increasedspecificity, as well as antibody class switching.

To summarize, optimal uptake of antigen by APC to elicit humoralimmunity, as well as specific CD4⁺ cytotoxic T cells, requires that theantigen be in native protein conformation (as presented subsequently tothe immune system upon natural infection) and recognized by naive Bcells bearing the appropriate membrane antibody. Native proteinconformation includes appropriate protein folding, glycosylation and anyother post-translational modifications necessary for optimal reactivitywith the receptors (immunoglobulin and possibly non-immunoglobulin) onAPC. In addition to the three dimensional structure of the expressedantigen required for recognition by specific antibody and elicitation ofthe required immune responses, the structure (and sequence) can beoptimized for increased protein stability outside the expressing cell,until the time when it is recognized by immune cells, including APCs.The reassembly (&/or one or more additional directed evolution methodsdescribed herein) and screening methods of the invention can be used tooptimize the antigen structure (and sequence) for subsequent processingafter uptake by APC so that intracellular processing results inderivation of the required peptide fragments for presentation on Class Ior Class II on APC and desired immune responses.

(g) Optimal Partitioning of the Nascent Antigen into the DesiredSubcellular Compartment or Compartments.

This can be directed by signal and trafficking signals embodied in theantigen sequence. It may be desirable for all of the antigen to besecreted from these cells; alternatively, all or part of the antigencould be directed to be expressed on the cell surface of these factorycells. Signals to direct vesicles containing the antigen to othersubcellular compartments for post-translational modifications, includingglycosylation, can be embodied in the antigen sequence.

(h) Optimal Display of the Antigen on the Cell Surface or OptimalRelease of the Antigen from the Cells.

A variation on items (f) and (g) is to design the expression of theantigen within the cytoplasm of the factory cell followed by lysis ofthat cell to release soluble antigen. Cell death can be engineered byexpression on the same genetic vaccine vector of an intracellularprotein that will elicit apoptosis. In this case, the timing of celldeath is balanced with the need for the cell to produce antigen, as wellas the potential deleterious effect of killing some cells in a designedprocess.

In combination, items (a)-(h) lead to a variety of scenarios for theoptimizing the longevity and extent of antigen expression. It is notalways desirable that the antigen be expressed for the longest time atthe highest level. In certain clinical applications, it will beimportant to have antigen expression that is short time-low expression,short time-high expression, long time-low expression, long time-highexpression or somewhere in between.

Plasmid AR can be designed to express one or more variants of a singleantigen gene or several quite different targets for immunization.Methods for obtaining optimized antigens for use in genetic vaccines aredescribed herein. Multiple antigens can be expressed from amonocistronic or multicistronic form of the vector.

2.4.2. Vector Components “CTL-DC”, “CTL-LC” and “CTL-MM”, Designed forOptimal Production of CTLs

Genetic vector components “CTL-DC”, “CTL-LC” and “CTL-MM” are designedto direct optimal production of cytotoxic CD8⁺ lymphocytes (CTLs) bydendritic cells (CTL-DC), Langerhan's cells (CTL-LC), and monocytes andmacrophages (CTL-MM) These vector components direct presentation ofoptimal antigen fragments in association with MHC Class I, therebyensuring maximal cytotoxic T cell immune responses. Cells transfectedwith CTL vector components can be considered as the direct activators ofthis arm of specific immunity that is usually critically important forprotection against viral diseases.

CTL vector components are typically designed to have one or more of thefollowing properties, each of which can be optimized using thestochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly methods of the invention:

(a) Optimal Vector Binding to, and Uptake by, the Chosen AntigenPresenting Cells (e.g., Dendritic Cells, Monocytes/Macrophages,Langerhan's Cells).

This is a critical property to differentiate CTL series vectors fromother vectors in the multicomponent DNA vaccine. CTL series vectorspreferably do not bind to or enter cells that are chosen to be theextracellular antigen expression host via AR vectors. This separation offunctions is critical, as the intracellular fate and trafficking ofantigen destined for stimulation of immune cells after release from anantigen expressing cell is quite different than the fate of antigendestined to be presented on the cell surface in association with MHCClass I. In the former case, antigen is directed via a signal secretionsequence to be delivered intact to the lumen of the rough endoplasmicreticulum (RER) and then secreted. In the latter case, antigen isdirected to remain in the cytoplasm and there be degraded into peptidefragments by the proteasomal system followed by delivery to the lumen ofthe RER for association with MHC Class I. These complexes of peptide andMHC Class I are then delivered to the cell surface for specificinteraction with CD8⁺ cytotoxic T cells. Vector components, and methodsfor obtaining optimized vector components, that are optimized fortargeting to desired cell types are described in

Optimizing Transcription of the Antigen Gene(s)

This can be accomplished by optimizing promoters, enhancers, introns,and the like, as discussed herein. Cell specific promoters are valuablein such vectors as an additional level of selectivity.

(b) Optimal Longevity of the mRNA.

Optimal 3′ and 5′ non-translated regions of the mRNA can be obtainedusing the methods of the invention.

(c) Optimal Translation of the mRNA.

Again, the stochastic (e.g. polynucleotide shuffling & interruptedsynthesis) and non-stochastic polynucleotide reassembly and selectionmethods of the invention can be used to obtain polynucleotide sequencesfor optimal ribosome binding and assembly of translational machinery, aswell as optimal codon preference.

(d) Optimal Protein Conformation.

In this case, the optimal protein conformation yields appropriatecytoplasmic proteolysis and production of the correct peptides forpresentation on MHC Class I and elicitation of the desired specific CTLresponses, rather than a conformation that will interact with specificantibody or other receptors on the surface of APC.

(e) Optimal Proteolysis to Generate the Correct Peptides.

The order of specific proteolytic cleavages will depend on the nature ofprotein folding and the nature of proteases either in the cytoplasm orin the proteasome.

(f) Optimal Transport of the Antigen Peptides Across the EndoplasmicReticulum Membrane to be Delivered into the RER Lumen.

This may be mediated by recognition of the peptides by TAP proteins orby other membrane transporters.

(h) optimal association of the peptides with the Class I-β2microglobulin complex and trafficking to the cell surface via thesecretory pathway.(i) Optimal Display of the MHC-Peptide Complex with Associated AccessoryMolecules for Recognition by Specific CTL.

Vector CTL can be designed to express one or more variants of a singleantigen gene or several different targets for immunization. Multipleoptimized antigens can be expressed from a monocistronic ormulticistronic form of the vector.

2.4.3. Vectors “M” Designed for Optimal Release of Immune Modulators

Vectors “M” are designed to direct optimal release of immune modulators,such as cytokines and other growth factors, from target cells. Targetcells can be either the predominant cell type in the immunized tissue orimmune cells such as dendritic cells (M-DC), Langerhan's cells (M-LC),monocytes & macrophages (M-MM)”. These vectors direct simultaneousexpression of optimal levels of several immune cell “modulators”(cytokines, growth factors, and the like) such that the immune responseis of the desired type, or combination of types, and of the desiredlevel. Cells transfected with M vectors can be considered as thedirectors of the nature of the vaccine immune response (CTL vs T_(H)1 vsT_(H)2 vs NK cell, etc.) and its magnitude. The properties of thesevectors reflect the nature of the cell in which the vectors are designedto operate. For example, the vectors are designed to bind to and enterthe desired cell type, and/or can have cell-specific regulated promotersthat drive transcription in the desired cell type. The vectors can alsobe engineered to direct maximal synthesis and release of the cellmodulator proteins from the target cells in the desired ratio.

“M” genetic vaccine vectors are typically designed to have one or moreof the following properties, each of which can be optimized using thestochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly methods of the invention:

(a) Optimal Vector Binding to and Uptake by the Chosen ModulatorExpressing Cell.

Suitable expressing cells include, for example, muscle cells, epithelialcells or other dominant (by number) cell types in the target tissue,antigen presenting cells (e.g. dendritic cells, monocytes/macrophages,Langerhans cells). This is a critical property which differentiates Mseries vectors from those designed to bind to and enter other cells.

(b) Optimal Transcription of the Immune Modulator Gene(s).

Again, promoters, enhancers, introns, and the like can be optimizedaccording to the methods of the invention. Cell specific promoters arevery valuable here as an additional level of selectivity.

(c) Optimal Longevity of the mRNA.

Optimal 3′ and 5′ non-translated regions of the mRNA can be obtainedusing the methods of the invention.

(d) Optimal Translation of the mRNA.

Again, the stochastic (e.g. polynucleotide shuffling & interruptedsynthesis) and non-stochastic polynucleotide reassembly and selectionmethods of the invention can be used to obtain polynucleotide sequencesfor optimal ribosome binding and assembly of translational machinery, aswell as optimal codon preference.

(e) Optimal Trafficking of the Modulator into the Lumen of the RER (Viaa Signal Secretion Sequence).

An alternative strategy for modulation of the immune response usesmembrane anchored modulators rather than secretion of soluble modulator.Anchored modulator can be retained on the surface of the synthesizingcell by, for example, a hydrophobic tail and phosphoinositol glycanlinkage.

(f) Optimal Protein Conformation for Each Modulator.

In this case, the optimal protein conformation is that which allowsextracellular modulator and/or cell membrane anchored modulator tointeract with the relevant receptor.

(g) The Ratio of Modulators and Their Type can be DeterminedEmpirically.

One will test sets of modulators that are known to work in concert todirect the immune response in the direction of a T_(H) response (e.g.,production of IL-2 and/or IFNγ) or T_(H)2 response (e.g., IL-4, IL-5,IL-13), for example. Vector M can be designed to express one or moremodulators. Optimized immunomodulators, and methods for obtainingoptimized immunomodulators, are described herein. These optimizedimmunomodulatory sequences are particularly suitable for use ascomponents of the multicomponent genetic vaccines of the invention.Multiple modulators can be expressed from a monocistronic ormulticistronic form of the vector.

2.4.4. Vectors “CK”, Designed to Direct Release of Chemokines

Genetic vaccine vectors designated “CK” are designed to direct optimalrelease of chemokines from target cells. Target cells can be either thepredominant cell type in the immunized tissue, or can be immune cellssuch as dendritic cells (CK-DC), Langerhan's cells (CK-LC), or monocytesand macrophages (CK-MM). These vectors typically direct simultaneousexpression of optimal levels of several chemokines such that therecruitment of immune cells to the site of immunization is optimal.Cells transfected with CK vectors can be considered as the trafficpolice, regulating the immune cells critical for the vaccine immuneresponse. The properties of these vectors reflect the nature of the cellin which the vectors are designed to operate. For example, the vectorsare designed to bind to and enter the desired cell type, and/or can havecell-specific regulated promoters that drive transcription in thedesired cell type. The vectors are also engineered to direct maximalsynthesis and release of the chemokines from the target cells in thedesired ratio. Genetic vaccine components, and methods for obtainingcomponents, that provide optimal release of chemokines are describedherein.

CK vectors are typically designed to have one or more of the followingproperties, each of which can be optimized using the stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly methods of the invention:

(a) Optimal Vector Binding to and Uptake by the Chosen ChemokineExpressing Cell.

Suitable cells include, for example, muscle cells, epithelial cells, orcell types that are dominant (by number) in the particular tissue ofinterest. Also suitable are antigen presenting cells (e.g. dendriticcells, monocytes and macrophages, Langerhans cells). This is a criticalproperty which differentiates CK series vectors from those designed tobind to and enter other cells.

(b) Optimal Transcription of the Chemokine Gene(s).

Again, promoters, enhancers, introns, and the like can be optimizedaccording to the methods of the invention.

Cell specific promoters are very valuable here as an additional level ofselectivity.

(c) Optimal Longevity of the mRNA.

Optimal 3′ and 5′ non-translated regions of the mRNA can be obtainedusing the methods of the invention.

(d) Optimal Translation of the mRNA.

Again, the stochastic (e.g. polynucleotide shuffling & interruptedsynthesis) and non-stochastic polynucleotide reassembly and selectionmethods of the invention can be used to obtain polynucleotide sequencesfor optimal ribosome binding and assembly of translational machinery, aswell as optimal codon preference.

(e) Optimal Trafficking of the Chemokine into the Lumen of the RER (Viaa Signal Secretion Sequence).

An alternative strategy for modulation of the immune response viarecruitment of cells will use membrane anchored chemokine rather thansecretion of soluble chemokine. Anchored chemokine will be retained onthe surface of the synthesizing cell by a hydrophobic tail andphosphoinositol glycan linkage.

(f) Optimal Protein Conformation for Each Chemokine.

In this case, the optimal protein conformation is that which allowsextracellular chemokine/cell membrane anchored chemokine to interactwith the relevant receptor.

(g) The Ratio of Diverse Chemokines can be Determined Empirically.

One can test sets of chemokines that are known to work in concert todirect recruitment of CTL, T_(H) cells, B cells, monocytes/macrophages,eosinophils, and/or neutrophils as appropriate.

Vector CK can be designed to express one or more chemokines. Multiplechemokines can be expressed from a monocistronic or multicistronic formof the vector.

2.4.5. Other Vectors

Genetic vaccines which contain one or more additional component vectormoieties are also provided by the invention. For example, the geneticvaccine can include a vector that is designed to specifically enterdendritic cells and Langerhans cells, and will migrate to the draininglymph nodes.

This Vector is Designed to Provide for Expression of the TargetAntigen(s), as Well as a Cocktail of Cytokines and Chemokines Relevantto Elicitation of the Desired Immune Response in the Node

Depending on the clinical goals and nature of the antigen, the vectorcan be optimized for relatively long lived expression of the targetantigen so that stimulation of the immune system is prolonged at thenode. Another example is a vector that specifically modulates MHCexpression in B cells. Such vectors are designed to specifically bind toand enter B cells, cells either resident in the injection site orattracted into the site. Within the B cell, this vector directs theassociation of antigen peptides derived from specific uptake of antigeninto the endocytic compartment of the cell to either association withClass I or Class II, hence directing the elicitation of specificimmunity via CD4⁺ T helper cells or CD8⁺ cytotoxic lymphocytes. Numerousmeans exist for this intracellular direction of the fate of processedpeptide that are discussed herein.

Examples of molecules that direct Class I presentation include tapasin,TAP-1 and TAP-2 (Koopman et al. (1997) Curr. Opin. Immunol. 9: 80-88),and those affecting Class II presentation include, for example,endosomal/lysosomal proteases (Peters (1997) Curr. Opin. Immunol. 9:89-96). Genetic vaccine components, and methods for obtainingcomponents, that provide optimized Class I presentation are describedherein. An optimal DNA vaccine could, for example, combine an AR vector(antigen release), a CTL-DC vector (CTL activation via dendritic cellpresentation of antigen peptide on MHC Class I), an M-MM vector forrelease of IL-12 and IFN-K from resident tissue macrophages, and a CKvector for recruitment of TH cells into the immunization site.

Directed Evolution Aid the Following DNA Vaccination Goals

DNA vaccination can be used for diverse goals that can include thefollowing, among others:

-   -   stimulation of a CTL response and/or humoral response ready to        react rapidly and aggressively against an invading bacterial or        viral pathogen at some time in the distant future    -   a continuous but non-aggressive response to prevent        inappropriate responses to allergens    -   a continuous non-aggressive and tolerization of immunity to an        autoantigen in autoimmune disease    -   elicitation of an aggressive CTL response as rapidly as possible        against tumor cell antigens    -   redirection of the immune response away from a strong but        inappropriate immune response to an on-going chronic infection        in the direction of desired responses to clear the pathogen        and/or prevent pathology.

These goals cannot always be met by the format of a single vector DNAvaccine, particularly wherein competing goals are embodied within oneDNA sequence. A multicomponent format allows the generation of aportfolio of DNA vaccine vectors, some of which will be reconstructed oneach occasion (e.g., those vectors containing antigen) while others willbe used as well characterized and understood reagents for numerousdifferent clinical applications (e.g., the same chemokine-expressingvector can be used in different situations).

2.5. Screening Methods

Screening Assay Varies Depending of Property for which Improvement isSought

Recombinant nucleic acid libraries that are obtained by the methodsdescribed herein are screened to identify those DNA segments that have aproperty which is desirable for genetic vaccination. The particularscreening assay employed will vary, as described below, depending on theparticular property for which improvement is sought. Typically, theexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) nucleic acid library isintroduced into cells prior to screening. If the stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly format employed is an in vivo format, thelibrary of recombinant DNA segments generated already exists in a cell.If the sequence reassembly (&/or one or more additional directedevolution methods described herein) is performed in vitro, therecombinant library is preferably introduced into the desired cell typebefore screening/selection. The members of the recombinant library canbe linked to an episome or virus before introduction or can beintroduced directly.

Cell Types

A wide variety of cell types can be used as a recipient of evolvedgenes. Cells of particular interest include many bacterial cell typesthat are used to deliver vaccines or vaccine antigens (Courvalin et al.(1995) C. R. Acad. Sci. 11118: 1207-12), both gram-negative andgram-positive, such as salmonella (Attridge et al. (1997) Vaccine 15:155-62), clostridium. (Fox et al. (1996) Gene Ther. 3: 173-8),lactobacillus, shigella (Sizemore et al. (1995) Science 270: 299-302),E. coli, streptococcus (Oggioni and Pozzi (1996) Gene 169: 85-90), aswell as mammalian cells, including human cells. In some embodiments ofthe invention, the library is amplified in a first host, and is thenrecovered from that host and introduced to a second host more amenableto expression, selection, or screening, or any other desirableparameter. The manner in which the library is introduced into the celltype depends on the DNA-uptake characteristics of the cell type, e.g.,having viral receptors, being capable of conjugation, or being naturallycompetent. If the cell type is unsusceptible to natural andchemical-induced competence, but susceptible to electroporation, onewould usually employ electroporation. If the cell type is unsusceptibleto electroporation as well, one can employ biolistics. The biolisticPDS-1000 Gene Gun (Biorad, Hercules, Calif.) uses helium pressure toaccelerate DNA-coated gold or tungsten microcarriers toward targetcells.

Competent or Potentially Competent Tissue

The process is applicable to a wide range of tissues, including plants,bacteria, fungi, algae, intact animal tissues, tissue culture cells, andanimal embryos. One can employ electronic pulse delivery, which isessentially a mild electroporation format for live tissues in animalsand patients (Zhao, Advanced Drug Delivery Reviews 17:257-262 (1995)).Novel methods for making cells competent are described in InternationalPatent Application PCT/US97/04494 (Publ. No. WO97/35957). Afterintroduction of the library of recombinant DNA genes, the cells areoptionally propagated to allow expression of genes to occur.

Identifying Cells that Contain a Vector Through Inclusion of aSelectable Marker Gene

In many assays, a means for identifying cells that contain a particularvector is necessary. Genetic vaccine vectors of all kinds can include aselectable marker gene. Under selective conditions, only those cellsthat express the selectable marker will survive.

Examples of Selectable Marker Genes

Examples of suitable markers include, the dihydrofolate reductase gene(DHFR), the thymidine kinase gene (TK), or prokaryotic genes conferringdrug resistance, gpt (xanthine-guanine phosphoribosyltransferase, whichcan be selected for with mycophenolic acid; neo (neomycinphosphotransferase), which can be selected for with G418, hygromycin, orpuromycin; and DHFR (dihydrofolate reductase), which can be selected forwith methotrexate (Mulligan & Berg; Southern & Berg (1982) J Mol. Appl.Genet. 1: 327).

Identifying Cells that Contain a Vector Through Inclusion of aScreenable Marker Gene

As an alternative to, or in addition to, a selectable marker, a geneticvaccine vector can include a screenable marker which, when expressed,confers upon a cell containing the vector a readily identifiablephenotype. For example, a gene that encodes a cell surface antigen thatis not normally present on the host cell is suitable. The detectionmeans can be, for example, an antibody or other ligand whichspecifically binds to the cell surface antigen. Examples of suitablecell surface antigens include any CD (cluster of differentiation)antigen (CD1 to CD163) from a species other than that of the host cellwhich is not recognized by host-specific antibodies. Other examplesinclude green fluorescent protein (GFP, see, e.g., Chalfie et al. (1994)Science 263:802-805; Crameri et al. (1996) Nature Biotechnol. 14:315-319; Chalfie et al. (1995) Photochem. Photobiol. 62:651-656; Olsonet al. (1995) J Cell. Biol. 130:639-650) and related antigens, severalof which are commercially available.

0.0.0. Screening for Vector Longevity or Translocation to Desired Tissue

For certain applications, it is desirable to identify those vectors withthe greatest longevity as DNA, or to identify vectors which end up intissues distant from the injection site. This can be accomplished byadministering to an animal a population of recombinant genetic vaccinevectors by the chosen route of administration and, at various timesthereafter excise the target tissue and recover vector from the tissueby standard molecular biology procedures. The recovered vector moleculescan be amplified in, for example, E. coli and/or by PCR in vitro. ThePCR amplification can involve further polynucleotide (e.g. gene,promoter, enhancer, intron, & the like) reassembly (optionally incombination with other directed evolution methods described herein),after which the derived selected population used for readministration toanimals and further improvement of the vector. After several rounds ofthis procedure, the selected vectors can be tested for their capacity toexpress the antigen in the correct conformation under the sameconditions as the vector was selected in vivo.

Methods for In Vitro Identification of Cells Expressing the DesiredAntigen

Because antigen expression is not part of the selection or screeningprocess described above, not all vectors obtained are capable ofexpressing the desired antigen. To overcome this drawback, the inventionprovides methods for identifying those vectors in a genetic vaccinepopulation that exhibit not only the desired tissue localization andlongevity of DNA integrity in vivo, but retention of maximal antigenexpression (or expression of other genes such as cytokines, chemokines,cell surface accessory molecules, MHC, and the like).

The methods involve in vitro identification of cells which express thedesired molecule using cells purified from the tissue of choice, underconditions that allow recovery of very small numbers of cells andquantitative selection of those with different levels of antigenexpression as desired.

Two embodiments of the invention are described, each of which uses alibrary of genetic vaccine vectors as the starting point. The goal ofeach method is to identify those vectors that exhibit the desiredbiological properties in vivo. The recombinant library represents apopulation of vectors that differ in known ways (e.g., a combinatorialvector library of different functional modules), or has randomlygenerated diversity generated either by insertion of random nucleotidestretches, or has been experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis) in vitro tointroduce low level mutations across all or part of the vector.

0.0.0.0. Selection for Expression of Cell Surface-Localized Antigen

In a first embodiment, the invention method involves selection forexpression of cell surface-localized antigen. The antigen gene isengineered in the vaccine vector library such that it has a region ofamino acids which is targeted to the cell membrane. For example, theregion can encode a hydrophobic stretch of C-terminal amino acids whichsignals the attachment of a phosphoinositol-glycan (PIG) terminus on theexpressed protein and directs the protein to be expressed on the surfaceof the transfected cell. With an antigen that is naturally a solubleprotein, this method will likely not affect the three dimensionalfolding of the protein in this engineered fusion with a new C-terminus.With an antigen that is naturally a transmembrane protein (e.g., asurface membrane protein on pathogenic viruses, bacteria, protozoa ortumor cells) there are at least two possibilities. First, theextracellular domain can be engineered to be in fusion with theC-terminal sequence for signaling PIG-linkage. Second, the protein canbe expressed in toto relying on the signaling of the host cell to directit efficiently to the cell surface. In a minority of cases, the antigenfor expression will have an endogenous PIG terminal linkage (e.g., someantigens of pathogenic protozoa).

Collection, Purification, Identification and Separation of Target Cells

The vector library is delivered in vivo and, after a suitable intervalof time tissue and/or cells from diverse target sites in the animal arecollected. Cells can be purified from the tissue using standard cellbiological procedures, including the use of cell specific surfacereactive monoclonal antibodies as affinity reagents. It is relativelyfacile to purify isolated epithelial cells from mucosal sites whereepithelium may have been inoculated or myoblasts from muscle. In someembodiments, minimal physical purification is performed prior toanalysis. It is sometimes desirable to identify and separate specificcell populations from various tissues, such as spleen, liver, bonemarrow, lymph node, and blood. Blood cells can be fractionated readilyby FACS to separate B cells, CD4⁺ or CD8⁺ T cells, dendritic cells,Langerhans cells, monocytes, and the like, using diverse fluorescentmonoclonal antibody reagents.

Identification and Purification of Cells Expressing the Antigen

Those cells expressing the antigen can be identified with a fluorescentmonoclonal antibody specific for the C-terminal sequence on PIG-linkedforms of the surface antigen. FACS analysis allows quantitativeassessment of the level of expression of the correct form of the antigenon the cell population. Cells expressing the maximal level of antigenare sorted and standard molecular biology methods used to recover theplasmid DNA vaccine vector that conferred this reactivity. Analternative procedure that allows purification of all those cellsexpressing the antigen (and that may be useful prior to loading onto acell sorter since antigen expressing cells may be a very small minoritypopulation), is to rosette or pan-purify the cells expressing surfaceantigen. Rosettes can be formed between antigen expressing cells anderythrocytes bearing covalently coupled antibody to the relevantantigen. These are readily purified by unit gravity sedimentation.Panning of the cell population over petri dishes bearing immobilizedmonoclonal antibody specific for the relevant antigen can also be usedto remove unwanted cells.

Cells expressing the required conformational structure of the targetantigen can be identified using specific conformationally-dependentmonoclonal antibodies that are known to react specifically with the samestructure as expressed on the target pathogen.

Using Several Monoclonal Antibodies in the Selection Process to Minimizethe Possibility of an Antigen which Reacts with High Affinity to theDiagnostic Antibody but does not Yield the Correct Conformation

Because one monoclonal antibody cannot define all aspects of correctfolding of the target antigen, one can minimize the possibility of anantigen which reacts with high affinity to the diagnostic antibody butdoes not yield the correct conformation as defined by that in which theantigen is found on the surface of the target pathogen or as secretedfrom the target pathogen. One way to minimize this possibility is to useseveral monoclonal antibodies, each known to react with differentconformational epitopes in the correctly folded protein, in theselection process. This can be achieved by secondary FACS sorting forexample.

The enriched plasmid population that successfully expressed sufficientof the antigen in the correct body site for the desired time is thenused as the starting population for another round of selection,incorporating gene reassembling (optionally in combination with otherdirected evolution methods described herein) to expand the diversity. Inthis manner, one recovers the desired biological activity encoded byplasmid from tissues in DNA vaccine-immunized animals.

This method can also provide the best in vivo selected vectors thatexpress immune accessory molecules that one may wish to incorporate intoDNA vaccine constructs. For example, if it is desired to express theaccessory protein B7.1 or B7.2 in antigen-presenting-cells (APC) (topromote successful presentation of antigen to T cells) one can sort APCisolated from different tissues (at or different to the inoculationsite) using commercially available monoclonal antibodies that recognizefunctional B7 proteins.

1.0.0.0. Selection for Expression of Secreted Antigen/Cytokine/Chemokine

Select Vectors that are Optimal in Inducing Secretion of SolubleProteins that can Affect the Qualitative and Quantitative Nature of anElicited Immune Response In Vivo

The invention also provides methods to identify plasmids in a geneticvaccine vector population that are optimal in secretion of solubleproteins that can affect the qualitative and quantitative nature of anelicited immune response. For example, the methods are useful forselecting vectors that are optimal for secretion of particularcytokines, growth factors and chemokines. The goal of the selection isto determine which particular combinations of cytokines, chemokines andgrowth factors, in combination with different promoters, enhancers,polyA tracts, introns, and the like, elicits the required immuneresponse in vivo.

Genes Encoding the Polypeptides are Typically Present in the VaccineVector Library in Combination with Optimal Signal Secretion Sequences(Proteins are Secreted from the Cells.)

Combinations of the genes for the soluble proteins of interest can bepresent in the vectors; transcription can be either from a singlepromoter, or the genes can be placed in multicistronic arrangements.Typically, the genes encoding the polypeptides are present in thevaccine vector library in combination with optimal signal secretionsequences, such that the expressed proteins are secreted from the cells.

Generating Vectors Capable of Secreting Different Combinations ofSoluble Factors In Vitro and Capable of Expressing Those Factors forDesired Lengths of Time.

The first step in these methods is to generate vectors that are capableof secreting high (or in some case low) levels of different combinationsof soluble factors in vitro and that will express those factors for ashort or long time as desired. This method allows one to select for andretain an inventory of plasmids which can be characterized by knownpatterns of soluble protein expression in known tissues for a knowntime. These vectors can then be tested individually for in vivoefficacy, after being placed in combination with the genetic vaccineantigen in an appropriate expression construct.

Delivery of Vector Library and Subsequent Collection, Testing, andPurification Using FACS Sorting, Affinity Panning, Rosetting, orMagnetic Bead Separation to Separate Cell Populations Prior toIdentification

The vector library is delivered to a test animal and, after a choseninterval of time, tissue and/or cells from diverse sites on the animalare collected. Cells are purified from the tissue using standard cellbiological procedures, which often include the use of cell specificsurface reactive monoclonal antibodies as affinity reagents. As is thecase for cell surface antigens described above, physical purification ofseparate cell populations can be performed prior to identification ofcells which express the desired protein. For these studies, the targetcells for expression of cytokines will most usually be APC or B cells orT cells rather than muscle cells or epithelial cells. In such cases FACSsorting by established methods will be preferred to separate thedifferent cell types. The different cell types described above may alsobe separated into relatively pure fractions using affinity panning,resetting or magnetic bead separation with panels of existing monoclonalantibodies known to define the surface membrane phenotype of murineimmune cells.

Identifying and Selecting Purified Cells Through Visual Inspection orFlow Cytometry For Use in Another Round Of Selection Incorporating GeneReassembling (Optionally in Combination with Other Directed EvolutionMethods Described Herein) to Expand the Diversity

Purified cells are plated onto agar plates under conditions thatmaintain cell viability. Cells expressing the required conformationalstructure of the target antigen are identified usingconformationally-dependent monoclonal antibodies that are known to reactspecifically with the same structure as expressed on the targetpathogen. Release of the relevant soluble protein from the cells isdetected by incubation with monoclonal antibody, followed by a secondaryreagent that gives a macroscopic signal (gold deposition, colordevelopment, fluorescence, luminescence). Cells expressing the maximallevel of antigen can be identified by visual inspection, the cell orcell colony picked and standard molecular biology methods used torecover the plasmid DNA vaccine vector that conferred this reactivity.Alternatively, flow cytometry can be used to identify and select cellsharboring plasmids that induce high levels of gene expression. Theenriched plasmid population that successfully expressed sufficient ofthe soluble factor in the correct body site for the desired time is thenused as the starting population for another round of selection,incorporating gene reassembling (optionally in combination with otherdirected evolution methods described herein) to expand the diversity, iffurther improvement is desired. In this manner, one recovers the desiredbiological activity encoded by plasmid from tissues in DNAvaccine-immunized animals.

Using Monoclonal Antibody to Confirm that the Initial Results fromScreening Still Hold when Several Conformational Epitopes are Probed

Several monoclonal antibodies, each known to react with differentconformational epitopes in the correctly folded cytokine, chemokine orgrowth factor, can be used to confirm that the initial results fromscreening with one monoclonal antibody reagent still hold when severalconformational epitopes are probed. In some cases the primary probe forfunctional cytokine released from the cell/cell colony in agar could bea soluble domain of the cognate receptor.

1.0.0. Flow Cytometry

Most of the Vector Module Libraries can be Assayed by Flow Cytometry toSelect Individual Human Tissue Culture Cells that Contain theExperimentally Generated Nucleic Acid Sequences that have the GreatestImprovement in the Desired Property

Flow cytometry provides a means to efficiently analyze the functionalproperties of millions of individual cells. The cells are passed throughan illumination zone, where they are hit by a laser beam; the scatteredlight and fluorescence is analyzed by computer-linked detectors. Flowcytometry provides several advantages over other methods of analyzingcell populations. Thousands of cells can be analyzed per second, with ahigh degree of accuracy and sensitivity. Gating of cell populationsallows multiparameter analysis of each sample. Cell size, viability, andmorphology can be analyzed without the need for staining. When dyes andlabeled antibodies are used, one can analyze DNA content, cell surfaceand intracytoplasmic proteins, and identify cell type, activation state,cell cycle stage, and detect apoptosis. Up to four colors (thus, fourseparate antigens stained with different fluorescent labels) and lightscatter characteristics can be analyzed simultaneously (four colorsrequires two-laser instrument; one-laser instrument can analyze threecolors). The expression levels of several genes can be analyzedsimultaneously, and importantly, flow cytometry-based cell sorting(“FACS sorting”) allows selection of cells with desired phenotypes. Mostof the vector module libraries, including the promoter, enhancer,intron, episomal origin of replication, expression level aspect ofantigen, bacterial origin and bacterial marker, can be assayed by flowcytometry to select individual human tissue culture cells that containthe reassembled (&/or subjected to one or more directed evolutionmethods described herein) nucleic acid sequences that have the greatestimprovement in the desired property. Typically the selection is for highlevel expression of a surface antigen or surrogate marker protein, asdiagrammed herein. The pool of the best individual sequences isrecovered from the cells selected by flow cytometry-based sorting. Anadvantage of this approach is that very large numbers (>107) can beevaluated in a single vial experiment.

2.0.0. Additional In Vitro Screening Methods

Screening for Improved Vaccination Properties Using Various In VitroTesting Methods Such as Screening for Improved Adjuvant Activity andImmunostimulatory Properties.

Genetic vaccine vectors and vector modules can be screened for improvedvaccination properties using various in vitro testing methods that areknown to those of skill in the art. For example, the optimized geneticvaccines can be tested for their effect on induction of proliferation ofthe particular lymphocyte type of interest, e.g., B cells, T cells, Tcell lines, and T cell clones. This type of screening for improvedadjuvant activity and immunostimulatory properties can be performedusing, for example, human or mouse cells.

Screening for Improved Vaccination Properties Using Various In VitroTesting Methods such as Screening for Cytokine Production (ELISA and/orCytoplasmic Cytokine Staining and Flow Cytometry) or for Alterations inthe Capacity of the Vectors to Direct T_(H)1/T_(H)2 Differentiation

A library of genetic vaccine vectors, e.g. obtained either frompolynucleotide reassembly (optionally in combination with other directedevolution methods described herein), or of vectors harboring genesencoding cytokines, costimulatory molecules etc.) can be screened forcytokine production (e.g., IL-2, IL-4, IL-5, IL-6, IL-10, IL-12, IL-13,IL-15, IFN-γ, TNF-α) by B cells, T cells, monocytes/macrophages, totalhuman PBMC, or (diluted) whole blood. Cytokines can be measured by ELISAor and cytoplasmic cytokine staining and flow cytometry (single-cellanalysis). Based on the cytokine production profile, one can screen foralterations in the capacity of the vectors to direct T_(H)1/T_(H)2differentiation (as evidenced, for example, by changes in ratios ofIL-4/IFN-γ, IL-4/IL-2, IL-5/IFN-γ, IL-5/IL-2, IL-13/IFN-γ, IL-13/IL-2).Induction of APC activation can be detected based on changes in surfaceexpression levels of activation antigens, such as B7-1 (CD80), 137-2(CD86), MHC class I and II, CD14, CD23, and Fc receptors, and the like.

Analyzing Genetic Vaccine Vectors for Their Capacity to Induce T CellActivation Through Isolating Spleen Cell of Infected Mice and Studyingthe Capacity of Cytotoxic T Lymphocytes to Lyse Infected, AutologousTarget Cells

In some embodiments, genetic vaccine vectors are analyzed for theircapacity to induce T cell activation. More specifically, spleen cellsfrom injected mice can be isolated and the capacity of cytotoxic Tlymphocytes to lyse infected, autologous target cells is studied. Thespleen cells are reactivated with the specific antigen in vitro. Inaddition, T helper cell differentiation is analyzed by measuringproliferation or production of T_(H)1 (IL-2 and IFN-γ) and T_(H)2 (IL-4and IL-S) cytokines by ELISA and directly in CD4⁺ T cells by cytoplasmiccytokine staining and flow cytometry.

Testing for Ability to Induce Humoral Immune Responses with AssaysUsing, for Example, Peripheral B Lymphocytes from Immunized Individualsor Other Assays Involving Detection of Antigen Expression by the TargetCells

Genetic vaccines and vaccine components can also be tested for abilityto induce humoral immune responses, as evidenced, for example, byinduction of B cell production of antibodies specific for an antigen ofinterest. These assays can be conducted using, for example, peripheral Blymphocytes from immunized individuals. Such assay methods are known tothose of skill in the art. Other assays involve detection of antigenexpression by the target cells. For example, FACS selection provides themost efficient method of identifying cells which produce a desiredantigen on the cell surface. Another advantage of FACS selection is thatone can sort for different levels of expression; sometimes lowerexpression may be desired. Another method involves panning usingmonoclonal antibodies on a plate. This method allows large numbers ofcells to be handled in a short time, but the method only selects forhighest expression levels. Capture by magnetic beads coated withmonoclonal antibodies provides another method of identifying cells whichexpress a particular antigen.

Screening for Ability to Inhibit Proliferation of Tumor Cell Lines InVitro

Genetic vaccines and vaccine components that are directed against cancercells can be screened for their ability to inhibit proliferation oftumor cell lines in vitro. Such assays are known in the art. Anindication of the efficacy of a genetic vaccine against, for example,cancer or an autoimmune disorder, is the degree of skin inflammationwhen the vector is injected into the skin of a patient or test animal.Strong inflammation is correlated with strong activation ofantigen-specific T cells. Improved activation of tumor-specific T cellsmay lead to enhanced killing of the tumors. In case of autoantigens, onecan add immunomodulators that skew the responses towards T_(H)2. Skinbiopsies can be taken, enabling detailed studies of the type of immuneresponse that occurs at the sites of each injection (in mice largenumbers of injections/vectors can be analyzed) Other suitable screeningmethods can involve detection of changes in expression of cytokines,chemokines, accessory molecules, and the like, by cells upon challengeby a library of genetic vaccine vectors.

Expressing the Recombinant Peptides or Polypeptides as Fusions with aProtein Displayed on the Surface of a Replicable Genetic Package

Various screening methods for particular applications are describedherein. In several instances, screening involves expressing therecombinant peptides or polypeptides encoded by the experimentallygenerated polynucleotides of the library as fusions with a protein thatis displayed on the surface of a replicable genetic package. Forexample, phage display can be used. See, e.g., Cwirla et al., Proc.Natl. Acad. Sci. USA 87: 6378-6382 (1990); Devlin et al., Science 249:404-406 (1990), Scott &#0000; Ladner et al., U.S. Pat. No. 5,571,698.Other replicable genetic packages include, for example, bacteria,eukaryotic viruses, yeast, and spores.

Purification and In Vitro Analysis of Recombinant Nucleic Acids andPolypeptides

Once stochastic (e.g. polynucleotide shuffling & interrupted synthesis)and/or non-stochastic polynucleotide reassembly has been performed, theresulting library of experimentally generated polynucleotides can besubjected to purification and preliminary analysis in vitro, in order toidentify the most promising candidate recombinant nucleic acids.Advantageously, the assays can be practiced in a high-throughput format.For example, to purify individual experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) recombinant antigens, clones can robotically picked into96-well formats, grown, and, if desired, frozen for storage.

Whole cell lysates (V-antigen), periplasmic extracts, or culturesupernatants (toxins) can be assayed directly by ELISA as describedbelow, but high throughput purification is sometimes also needed.Affinity chromatography using immobilized antibodies or incorporation ofa small nonimmunogenic affinity tag such as a hexahistidine peptide withimmobilized metal affinity chromatography will allow rapid proteinpurification. High binding-capacity reagents with 96-well filter bottomplates provide a high throughput purification process. The scale ofculture and purification will depend on protein yield, but initialstudies will require less than 50 micrograms of protein. Antigensshowing improved properties can be purified in larger scale by FPLC forre-assay and animal challenge studies.

In some embodiments, the experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis)antigen-encoding polynucleotides are assayed as genetic vaccines.Genetic vaccine vectors containing the experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) antigen sequences can be prepared using robotic colonypicking and subsequent robotic plasmid purification. Robotic plasmidpurification protocols are available that allow purification of 600-800plasmids per day. The quantity and purity of the DNA can also beanalyzed in 96-well plates, for example. In a presently preferredembodiment, the amount of DNA in each sample is robotically normalized,which can significantly reduce the variation between different batchesof vectors.

Once the proteins and/or nucleic acids are picked and purified asdesired, they can be subjected to any of a number of in vitro analysismethods. Such screenings include, for example, phage display, flowcytometry, and ELISA assays to identify antigens that are efficientlyexpressed and have multiple epitopes and a proper folding pattern. Inthe case of bacterial toxins, the libraries may also be screened forreduced toxicity in mammalian cells.

As one example, to identify recombinant antigens that arecross-reactive, one can use a panel of monoclonal antibodies forscreening. A humoral immune response generally targets multiple regionsof antigenic proteins. Accordingly, monoclonal antibodies can be raisedagainst various regions of immunogenic proteins (Alving et al. (1995)Immunol. Rev. 145: 5). In addition, there are several examples ofmonoclonal antibodies that only recognize one strain of a givenpathogen, and by definition, different serotypes of pathogens arerecognized by different sets of antibodies. For example, a panel ofmonoclonal antibodies have been raised against VEE envelope proteins,thus providing a means to recognize different subtypes of the virus(Roehrig and Bolin (1997) J Clin. Microbiol. 35: 1887). Such antibodies,combined with phage display and ELISA screening, can be used to enrichrecombinant antigens that have epitopes from multiple pathogen strains.Flow cytometry based cell sorting will further allow for the selectionof variants that are most efficiently expressed.

Phage display provides a powerful method for selecting proteins ofinterest from large libraries (Bass et al. (1990) Proteins: Struct.Funct. Genet. 8: 309; Lowman and Wells (1991) Methods: A Companion toMethods Enz. 3(3); 205-216. Lowman and Wells (1993) J Mol. Biol. 234;564-578). Some recent reviews on the phage display technique include,for example, McGregor (1996) Mol. Biotechnol. 6(2):15 5-62; Dunn (1996)Curr. Opin. Biotechnol. 7(5):547-53; Hill et al. (1996) Mol Microbiol20(4):685-92; Phage Display of Peptides and Proteins: A LaboratoryManual. BK. Kay, J. Winter, J, McCafferty eds., Academic Press 1996;O'Neil et al. (1995) Curr. Opin. Struct. Biol. 5(4):443-9; Phizicky etal. (1995) Microbiol Rev. 59(1):94-123; Clackson et al. (1994) TrendsBiotechnol. 12(5):173-84; Felici et al. (1995) Biotechnol. Annu. Rev. 1:149-83; Burton (1995) Immunotechnology 1(2):87-94.) See, also, Cwirla etal., Proc. Natl. Acad. Sci. USA 87: 6378-6382 (1990); Devlin et al.,Science 249: 404-406 (1990), Scott & Smith, Science 249: 386-388 (1990);Ladner et al., U.S. Pat. No. 5,571,698. Each phage particle displays aunique variant protein on its surface and packages the gene encodingthat particular variant. The experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) genes for the antigens are fused to a protein that isexpressed on the phage surface, e.g., gene III of phage M13, and clonedinto phagemid vectors. In a presently preferred embodiment, asuppressible stop codon (e.g., an amber stop codon) separates the genesso that in a suppressing strain of E. coli, the antigen-gIIIp fusion isproduced and becomes incorporated into phage particles upon infectionwith M13 helper phage. The same vector can direct production of theunfused antigen alone in a nonsuppressing E. coli for proteinpurification.

Most Frequently Used Genetic Packages for Display Libraries

The genetic packages most frequently used for display libraries arebacteriophage, particularly filamentous phage, and especially phage M13,Fd and F1. Most work has involved inserting libraries encodingpolypeptides to be displayed into either gIII or gVIII of these phageforming a fusion protein. See, e.g., Dower, WO 91/19818; Devlin, WO91/18989; MacCafferty, WO 92/01047 (gene HI); Huse, WO 92/06204; Kang,WO 92/18619 (gene VIII). Such a fusion protein comprises a signalsequence, usually but not necessarily, from the phage coat protein, apolypeptide to be displayed and either the gene III or gene VIII proteinor a fragment thereof. Exogenous coding sequences are often inserted ator near the N-terminus of gene III or gene VIII although other insertionsites are possible.

Use of Eukaryotic Viruses to Display Polypeptides

Eukaryotic viruses can be used to display polypeptides in an analogousmanner. For example, display of human heregulin fused to gp70 of Moloneymurine leukemia virus has been reported by Han et al., Proc. Natl. Acad.Sci. USA 92: 9747-9751 (1995). Spores can also be used as replicablegenetic packages. In this case, polypeptides are displayed from theouter surface of the spore. For example, spores from B. subtilis havebeen reported to be suitable. Sequences of coat proteins of these sporesare provided by Donovan et al., J. Mol. Biol. 196, 1-10 (1987). Cellscan also be used as replicable genetic packages. Polypeptides to bedisplayed are inserted into a gene encoding a cell protein that isexpressed on the cells surface. Bacterial cells including Salmonellatyphimurium, Bacillus subtilis, Pseudomonas aeruginosa, Vibrio cholerae,Klebsiella pneumonia, Neisseria gonorrhoeae, Neisseria meningitidis,Bacteroides nodosus, Moraxella bovis, and especially Escherichia coliare preferred. Details of outer surface proteins are discussed by Ladneret al., U.S. Pat. No. 5,571,698 and references cited therein. Forexample, the lamB, protein of E. coli is suitable.

Establishment of a Physical Association Between Polypeptides and TheirGenetic Material

A basic concept of display methods that use phage or other replicablegenetic package is the establishment of a physical association betweenDNA encoding a polypeptide to be screened and the polypeptide. Thisphysical association is provided by the replicable genetic package,which displays a polypeptide as part of a capsid enclosing the genome ofthe phage or other package, wherein the polypeptide is encoded by thegenome. The establishment of a physical association between polypeptidesand their genetic material allows simultaneous mass screening of verylarge numbers of phage bearing different polypeptides. Phage displayinga polypeptide with affinity to a target, e.g., a receptor, bind to thetarget and these phage are enriched by affinity screening to the target.The identity of polypeptides displayed from these phage can bedetermined from their respective genomes.

Using these methods a polypeptide identified as having a bindingaffinity for a desired target can then be synthesized in bulk byconventional means, or the polynucleotide that encodes the peptide orpolypeptide can be used as part of a genetic vaccine.

Variants with specific binding properties, in this case binding tofamily-specific antibodies, are easily enriched by panning withimmobilized antibodies. Antibodies specific for a single family are usedin each round of panning to rapidly select variants that have multipleepitopes from the antigen families. For example, A-family specificantibodies can be used to select those experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) clones that display A-specific epitopes in the first roundof panning. A second round of panning with B-specific antibodies willselect from the “A” clones those that display both A- and B-specificepitopes. A third round of panning with C-specific antibodies willselect for variants with A, B, and C epitopes. A continual selectionexists during this process for clones that express well in E. coli andthat are stable throughout the selection. Improvements in factors suchas transcription, translation, secretion, folding and stability areoften observed and will enhance the utility of selected clones for usein vaccine production.

Phage ELISA methods can be used to rapidly characterize individualvariants. These assays provide a rapid method for quantitation ofvariants without requiring purification of each protein. Individualclones are arrayed into 96-well plates, gown, and frozen for storage.Cells in duplicate plates are infected with helper phage, grownovernight and pelleted by centrifugation. The supernatants containingphage displaying particular variants are incubated with immobilizedantibodies and bound clones are detected by anti-M13 antibodyconjugates. Titration series of phage particles, immobilized antigen,and/or soluble antigen competition binding studies are all highlyeffective means to quantitate protein binding. Variant antigensdisplaying multiple epitopes will be further studied in appropriateanimal challenge models.

Several groups have reported an in vitro ribosome display system for thescreening and selection of mutant proteins with desired properties fromlarge libraries. This technique can be used similarly to phage displayto select or enrich for variant antigens with improved properties suchas broad cross reactivity to antibodies and improved folding (see, e.g.,Hanes et al. (1997) Proc. Nat'l. A cad. Sci. USA 94(10):493 7-42;Mattheakis et al. (1994) Proc. Nat. 7. Acad. Sci. USA 91(19):9022-6; Heet al. (1997) Nucl. Acids Res. (24):5132-4; Nemoto et al. (1997) FEBSLett. 414(2):405-8).

Other display methods exist to screen antigens for improved propertiessuch as increased expression levels, broad cross reactivity, enhancedfolding and stability. These include, but are not limited to display ofproteins on intact E. coli or other cells (e.g., Francisco et al. (1993)Proc. Nat'l. Acad. Sci. USA 90: 1044-10448; Lu et al. (1995)Biotechnology 13: 366-372). Fusions of experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) antigens to DNA-binding proteins can link the antigenprotein to its gene in an expression vector (Schatz et al. (1996)Methods Enzymol. 267: 171-91; Gates et al. (1996) J Mol. Biol. 255:373-86.) The various display methods and ELISA assays can be used toscreen for experimentally evolved (e.g. by polynucleotide reassembly&/or polynucleotide site-saturation mutagenesis) antigens with improvedproperties such as presentation of multiple epitopes, improvedimmunogenicity, increased expression levels, increased folding rates andefficiency, increased stability to factors such as temperature, buffers,solvents, improved purification properties, etc. Selection ofexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) antigens with improvedexpression, folding, stability and purification profile under a varietyof chromatographic conditions can be very important improvements toincorporate for the vaccine manufacturing process. To identifyrecombinant antigenic polypeptides that exhibit improved expression in ahost cell, flow cytometry is a useful technique.

Flow cytometry provides a method to efficiently analyze the functionalproperties of millions of individual cells. One can analyze theexpression levels of several genes simultaneously, and flowcytometry-based cell sorting allows for the selection of cells thatdisplay properly expressed antigen variants on the cell surface or inthe cytoplasm. Very large numbers (>10⁷) of cells can be evaluated in asingle vial experiment, and the pool of the best individual sequencescan be recovered from the sorted cells. These methods are particularlyuseful in the case of, for example, Hantaan virus glycoproteins, whichare generally very poorly expressed in mammalian cells. This approachprovides a general solution to improve expression levels of pathogenantigens in mammalian cells, a phenomenon that is critical for thefunction of genetic vaccines.

To use flow cytometry to analyze polypeptides that are not expressed onthe cell surface, one can engineer the experimentally generatedpolynucleotides in the library such that the polynucleotide is expressedas a fusion protein that has a region of amino acids which is targetedto the cell membrane. For example, the region can encode a hydrophobicstretch of C-terminal amino acids which signals the attachment of aphosphoinositol-glycan (PIG) terminus on the expressed protein anddirects the protein to be expressed on the surface of the transfectedcell (Whitehorn et al. (1995) Biotechnology (NY) 13:1215-9). With anantigen that is naturally a soluble protein, this method will likely notaffect the three dimensional folding of the protein in this engineeredfusion with a new C-terminus. With an antigen that is naturally atransmembrane protein (e.g., a surface membrane protein on pathogenicviruses, bacteria, protozoa or tumor cells) there are at least twopossibilities.

First, the extracellular domain can be engineered to be in fusion withthe C-terminal sequence for signaling PIG-linkage. Second, the proteincan be expressed in toto relying on the signaling of the host cell todirect it efficiently to the cell surface. In a minority of cases, theantigen for expression will have an endogenous PIG terminal linkage(e.g., some antigens of pathogenic protozoa).

Those cells expressing the antigen can be identified with a fluorescentmonoclonal antibody specific for the C-terminal sequence on PIG-linkedforms of the surface antigen. FACS analysis allows quantitativeassessment of the level of expression of the correct form of the antigenon the cell population. Cells expressing the maximal level of antigenare sorted and standard molecular biology methods are used to recoverthe plasmid DNA vaccine vector that conferred this reactivity. Analternative procedure that allows purification of all those cellsexpressing the antigen (and that may be useful prior to loading onto acell sorter since antigen expressing cells may be a very small minoritypopulation), is to rosette or pan-purify the cells expressing surfaceantigen. Rosettes can be formed between antigen expressing cells anderythrocytes bearing covalently coupled antibody to the relevantantigen. These are readily purified by unit gravity sedimentation.Panning of the cell population over petri dishes bearing immobilizedmonoclonal antibody specific for the relevant antigen can also be usedto remove unwanted cells.

In the high throughput assays of the invention, it is possible to screenup to several thousand different experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) variants in a single day. For example, each well of amicrotiter plate can be used to run a separate assay, or, ifconcentration or incubation time effects are to be observed, every 5-10wells can test a single variant. Thus, a single standard microtiterplate can assay about 100 (e.g., 96) reactions. If 1536 well plates areused, then a single plate can easily assay from about 100 to about 1500different reactions. It is possible to assay several different platesper day; assay screens for up to about 6,000-20,000 different assays(i.e., involving different nucleic acids, encoded proteins,concentrations, etc.) is possible using the integrated systems of theinvention. More recently, microfluidic approaches to reagentmanipulation have been developed, e.g., by Caliper Technologies (PaloAlto, Calif.).

In one aspect, library members, e.g., cells, viral plaques, or the like,are separated on solid media to produce individual colonies (orplaques). Using an automated colony picker (e.g., the Q-bot, Genetix,U.K.), colonies or plaques are identified, picked, and up to 10,000different mutants inoculated into 96 well microtiter dishes, optionallycontaining glass balls in the wells to prevent aggregation. The Q-botdoes not pick an entire colony but rather inserts a pin through thecenter of the colony and exits with a small sampling of cells (orviruses in plaque applications). The time the pin is in the colony, thenumber of dips to inoculate the culture medium, and the time the pin isin that medium each effect inoculum size, and each can be controlled andoptimized. The uniform process of the Q-bot decreases human handlingerror and increases the rate of establishing cultures (roughly 10,000/4hours). These cultures are then shaken in a temperature and humiditycontrolled incubator. The glass balls in the microtiter plates act topromote uniform aeration of cells dispersal of cells, or the like,similar to the blades of a fermentor. Clones from cultures of interestcan be cloned by limiting dilution. Plaques or cells constitutinglibraries can also be screened directly for production of proteins,either by detecting hybridization, protein activity, protein binding toantibodies, or the like.

The ability to detect a subtle increase in the performance of aexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) library member over that ofa parent strain relies on the sensitivity of the assay. The chance offinding the organisms having an improvement in ability to induce animmune response is increased by the number of individual mutants thatcan be screened by the assay. To increase the chances of identifying apool of sufficient size, a prescreen that increases the number ofmutants processed by 10-fold can be used. The goal of the prescreen willbe to quickly identify mutants having equal or better product titersthan the parent strain(s) and to move only these mutants forward toliquid cell culture for subsequent analysis.

A number of well known robotic systems have also been developed forsolution phase chemistries useful in assay systems. These systemsinclude automated workstations like the automated synthesis apparatusdeveloped by Takeda Chemical Industries, LTD. (Osaka, Japan) and manyrobotic systems utilizing robotic arms (Zymate II, Zymark Corporation,Hopkinton, Mass.; Orca, Hewlett-Packard, Palo Alto, Calif.) which mimicthe manual synthetic operations performed by a scientist. Any of theabove devices are suitable for use with the present invention, e.g., forhigh-throughput screening of molecules encoded by codon-altered nucleicacids. The nature and implementation of modifications to these devices(if any) so that they can operate as discussed herein with reference tothe integrated system will be apparent to persons skilled in therelevant art.

High throughput screening systems are commercially available (see, e.g.,Zymark Corp., Hopkinton, Mass.; Air Technical Industries, Mentor, Ohio;Beckman Instruments, Inc. Fullerton, Calif.; Precision Systems, Inc.,Natick, Mass., etc.). These systems typically automate entire proceduresincluding all sample and reagent pipetting, liquid dispensing, timedincubations, and final readings of the microplate in detector(s)appropriate for the assay. These configurable systems provide highthroughput and rapid start up as well as a high degree of flexibilityand customization.

The manufacturers of such systems provide detailed protocols of thevarious high throughput screening systems. Thus, for example, ZymarkCorp. provides technical bulletins describing screening systems fordetecting the modulation of gene transcription, ligand binding, and thelike. Microfluidic approaches to reagent manipulation have also beendeveloped, e.g., by Caliper Technologies (Palo Alto, Calif.).

Optical images viewed (and, optionally, recorded) by a camera or otherrecording device (e.g., a photodiode and data storage device) areoptionally further processed in any of the embodiments herein, e.g., bydigitizing the image and/or storing and analyzing the image on acomputer. As noted above, in some applications, the signals resultingfrom assays are florescent, making optical detection approachesappropriate in these instances. A variety of commercially availableperipheral equipment and software is available for digitizing, storingand analyzing a digitized video or digitized optical image, e.g., usingPC (Intel x86 or Pentium chip-compatible DOS, OS2 WINDOWS, WINDOWS NT orVIMOWS95 based machines), MACINTOSH, or LTNIX based (e.g., SLJN workstation) computers.

One conventional system carries light from the assay device to a cooledcharge-coupled device (CCD) camera, in common use in the art. A CCDcamera includes an array of picture elements (pixels). The light fromthe specimen is imaged on the CCD. Particular pixels corresponding toregions of the specimen (e.g., individual hybridization sites on anarray of biological polymers) are sampled to obtain light intensityreadings for each position. Multiple pixels are processed in parallel toincrease speed. The apparatus and methods of the invention are easilyused for viewing any sample, e.g., by fluorescent or dark fieldmicroscopic techniques.

Integrated systems for analysis in the present invention typicallyinclude a digital computer with high-throughput liquid control software,image analysis software, data interpretation software, a robotic liquidcontrol armature for transferring solutions from a source to adestination operably linked to the digital computer, an input device(e.g., a computer keyboard) for entering data to the digital computer tocontrol high throughput liquid transfer by the robotic liquid controlarmature and, optionally, an image scanner for digitizing label signalsfrom labeled assay component. The image scanner interfaces with theimage analysis software to provide a measurement of optical intensity.Typically, the intensity measurement is interpreted by the datainterpretation software to show whether the optimized recombinantantigenic polypeptide products are produced.

3.0.0. Antigen Library Immunization

In a presently preferred embodiment, antigen library immunization (ALI)is used to identify optimized recombinant antigens that have improvedimmunogenicity. ALI involves introduction of the library of recombinantantigen-encoding nucleic acids, or the recombinant antigens encoded bythe experimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) nucleic acids, into a testanimal. The animals are then subjected to in vivo challenge using livepathogens. Neutralizing antibodies and cross-protective immune responsesare studied after immunization with the entire libraries, pools and/orindividual antigen variants.

Methods of immunizing test animals are well known to those of skill inthe art. In presently preferred embodiments, test animals are immunizedtwice or three times at two week intervals. One week after the lastimmunization, the animals are challenged with live pathogens (ormixtures of pathogens), and the survival and symptoms of the animals isfollowed. Immunizations using test animal challenge are described in,for example, Roggenkamp et al. (1997) Infect. Immun. 65: 446; Woody etal. (1997) Vaccine 2: 133; Agren et al. (1997) J Immunol. 158: 3936;Konishi et al. (1992) Virology 190: 454; Kinney et al. (1988) J Virol.62: 4697; Iacono-Connors et al. (1996) Virus Res. 43: 125; Kochel et al.(1997) Vaccine 15: 547; and Chu et al. (1995) J Virol. 69: 6417.

The immunizations can be performed by injecting either theexperimentally generated polynucleotides themselves, i.e., as a geneticvaccine, or by immunizing the animals with polypeptides encoded by theexperimentally generated polynucleotides. Bacterial antigens aretypically screened primarily as recombinant proteins, whereas viralantigens are preferably analyzed using genetic vaccinations.

To dramatically reduce the number of experiments required to identifyindividual antigens having improved immunogenic properties, one can usepooling and deconvolution, as diagrammed herein. Pools of recombinantnucleic acids, or polypeptides encoded by the recombinant nucleic acids,are used to immunize test animals. Those pools that result in protectionagainst pathogen challenge are then subdivided and subjected toadditional analysis. The high throughput in vitro approaches describedabove can be used to identify the best candidate sequences for the invivo studies.

The challenge models that can be used to screen for protective antigensinclude pathogen and toxin models, such as Yersinia bacteria, bacterialtoxins (such as Staphylococcal and Streptococcal enterotoxins, E.coli/V. cholerae enterotoxins), Venezuelan equine encephalitis virus(VEE), Flaviviruses (Japanese encephalitis virus, Tick-borneencephalitis virus, Dengue virus), Hantaan virus, Herpes simplex,influenza virus (e.g., Influenza A virus), Vesicular Steatites Virus,Pseudomonas aeruginosa, Salmonella typhimurium, Escherichia coli,Klebsiella pneumoniae, Toxoplasma gondii, Plasmodium yoeliii, Herpessimplex, influenza virus (e.g., Influenza A virus), and VesicularSteatites Virus. However, the test animals can also be challenged withtumor cells to enable screening of antigens that efficiently protectagainst malignancies. Individual experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) antigens or pools of antigens are introduced into theanimals intradermally, intramuscularly, intravenously, intratracheally,anally, vaginally, orally, or intraperitoneally and antigens that canprevent the disease are chosen, when desired, for further rounds ofreassembly (optionally in combination with other directed evolutionmethods described herein) and selection. Eventually, the most potentantigens, based on in vivo data in test animals and comparative in vitrostudies in animals and man, are chosen for human trials, and theircapacity to prevent and treat human diseases is investigated.

In some embodiments, antigen library immunization and pooling ofindividual clones is used to immunize against a pathogen strain that wasnot included in the sequences that were used to generate the library.The level of crossprotection provided by different strains of a givenpathogen can vary significantly. However, homologous titer is alwayshigher than heterologous titer. Pooling and deconvolution is especiallyefficient in models where minimal protection is provided by thewild-type antigens used as starting material for reassembly (optionallyin combination with other directed evolution methods described herein).This approach can be taken, for example, when evolving the V-antigen ofYersinae or Hantaan virus glycoproteins.

In some embodiments, the desired screening involves analysis of theimmune response based on immunological assays known to those skilled inthe art. Typically, the test animals are first immunized and blood ortissue samples are collected for example one to two weeks after the lastimmunization. These studies enable one to measure immune parameters thatcorrelate to protective immunity, such as induction of specificantibodies (particularly IgG) and induction of specific T lymphocyteresponses, in addition to determining whether an antigen or pools ofantigens provides protective immunity.

Spleen cells or peripheral blood mononuclear cells can be isolated fromimmunized test animals and measured for the presence of antigen-specificT cells and induction of cytokine synthesis. ELISA, ELISPOT andcytoplasmic cytokine staining, combined with flow cytometry, can providesuch information on a single-cell level.

Common immunological tests that can be used to identify the efficacy ofimmunization include antibody measurements, neutralization assays andanalysis of activation levels or frequencies of antigen presenting cellsor lymphocytes that are specific for the antigen or pathogen. The testanimals that can be used in such studies include, but are not limitedto, mice, rats, guinea pigs, hamsters, rabbits, cats, dogs, pigs andmonkeys.

Monkey is a particularly useful test animal because the MHC molecules ofmonkeys and humans are very similar. Virus neutralization assays areuseful for detection of antibodies that not only specifically bind tothe pathogen, but also neutralize the function of the virus. Theseassays are typically based on detection of antibodies in the sera ofimmunized animal and analysis of these antibodies for their capacity toinhibit viral growth in tissue culture cells. Such assays are known tothose skilled in the art. One example of a virus neutralization assay isdescribed by Dolin R (J. Infect. Dis. 1995, 172:1175-83). Virusneutralization assays provide means to screen for antigens that alsoprovide protective immunity.

In some embodiments, experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis) antigens arescreened for their capacity to induce T cell activation in vivo. Morespecifically, peripheral blood mononuclear cells or spleen cells frominjected mice can be isolated and the capacity of cytotoxic Tlymphocytes to lyse infected, autologous target cells is studied. Thespleen cells can be reactivated with the specific antigen in vitro. Inaddition, T helper cell activation and differentiation is analyzed bymeasuring cell proliferation or production of T_(H) (IL-2 and IFN-γ) andT_(H)2 (IL-4 and IL-5) cytokines by ELISA and directly in CD4+ T cellsby cytoplasmic cytokine staining and flow cytometry. Based on thecytokine production profile, one can also screen for alterations in thecapacity of the antigens to direct T_(H)1/T_(H)2 differentiation (asevidenced, for example, by changes in ratios of IL-4/IFN-γ, IL-4/IL-2,IL-5/IFN-γ, IL-5/IL-2, IL-13/IFN-γ, IL-13/IL-2). The analysis of the Tcell activation induced by the antigen variants is a very usefulscreening method, because potent activation of specific T cells in vivocorrelates to induction of protective immunity.

The frequency of antigen-specific CD8+ T cells in vivo can also bedirectly analyzed using tetramers of MHC class I molecules expressingspecific peptides derived from the corresponding pathogen antigens (Oggand McMichael, Curr. Opin. Immunol. 1998, 10:393-6; Altman et al.,Science 1996, 274:94-6). The binding of the tetramers can be detectedusing flow cytometry, and will provide information about the efficacy ofthe experimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) antigens to induceactivation of specific T cells. For example, flow cytometry and tetramerstainings provide an efficient method of identifying T cells that arespecific to a given antigen or peptide. Another method involves panningusing plates coated with tetramers with the specific peptides. Thismethod allows large numbers of cells to be handled in a short time, butthe method only selects for highest expression levels. The higher thefrequency of antigen-specific T cells in vivo is, the more efficient theimmunization has been, enabling identification of the antigen variantsthat have the most potent capacity to induce protective immuneresponses. These studies are particularly useful when conducted inmonkeys, or other primates, because the MHC class I molecules of humansmimic those of other primates more closely than those of mice.

Measurement of the activation of antigen presenting cells (APC) inresponse to immunization by antigen variants is another useful screeningmethod. Induction of APC activation can be detected based on changes insurface expression levels of activation antigens, such as 137-1 (CD80).137-2 (CD86), MHC class I and II, CD14, CD23, and Fc receptors, and thelike.

Experimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) cancer antigens that inducecytotoxic T cells that have the capacity to kill cancer cells can beidentified by measuring the capacity of T cells derived from immunizedanimals to kill cancer cells in vitro. Typically the cancer cells arefirst labeled with radioactive isotopes and the release of radioactivityis an indication of tumor cell killing after incubation in the presenceof T cells from immunized animals. Such cytotoxicity assays are known inthe art.

An indication of the efficacy of an antigen to activate T cells specificfor, for example, cancer antigens, allergens or autoantigens, is alsothe degree of skin inflammation when the antigen is injected into theskin of a patient or test animal. Strong inflammation is correlated withstrong activation of antigen-specific T cells. Improved activation oftumor-specific T cells may lead to enhanced killing of the tumors. Incase of autoantigens, one can add immunomodulators that skew theresponses towards T_(H)2, whereas in the case of allergens a T_(H)1response is desired. Skin biopsies can be taken, enabling detailedstudies of the type of immune response that occurs at the sites of eachinjection (in mice and monkeys large numbers of injections/antigens canbe analyzed). Such studies include detection of changes in expression ofcytokines, chemokines, accessory molecules, and the like, by cells uponinjection of the antigen into the skin.

To screen for antigens that have optimal capacity to activateantigen-specific T cells, peripheral blood mononuclear cells frompreviously infected or immunized humans individuals can be used. This isa particularly useful method, because the MHC molecules that willpresent the antigenic peptides are human MHC molecules. Peripheral bloodmononuclear cells or purified professional antigen-presenting cells(APCs) can be isolated from previously vaccinated or infectedindividuals or from patients with acute infection with the pathogen ofinterest. Because these individuals have increased frequencies ofpathogen-specific T cells in circulation, antigens expressed in PBMCs orpurified APCs of these individuals will induce proliferation andcytokine production by antigen-specific CD4+ and CD8+ T cells. Thus,antigens that simultaneously harbor epitopes from several antigens canbe recognized by their capacity to stimulate T cells from variouspatients infected or immunized with different pathogen antigens, cancerantigens, autoantigens or allergens. One buffy coat derived from a blooddonor contains lymphocytes from 0.5 liters of blood, and up to 10⁴ PBMCcan be obtained, enabling very large screening experiments using T cellsfrom one donor.

When healthy vaccinated individuals (lab volunteers) are studied, onecan make EBV-transformed B cell lines from these individuals. These celllines can be used as antigen presenting cells in subsequent experimentsusing blood from the same donor; this reduces interassay anddonor-to-donor variation. In addition, one can make antigen-specific Tcell clones, after which antigen variants are introduced to EBVtransformed B cells. The efficiency with which the transformed B cellsinduce proliferation of the specific T cell clones is then studied. Whenworking with specific T cell clones, the proliferation and cytokinesynthesis responses are significantly higher than when using totalPBMCs, because the frequency of antigen-specific T cells among PBMC isvery low.

CTL epitopes can be presented by most cells types since the class Imajor histocompatibility complex (MHC) surface glycoproteins are widelyexpressed. Therefore, transfection of cells in culture by libraries ofexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) antigen sequences inappropriate expression vectors can lead to class I epitope presentation.If specific CTLs directed to a given epitope have been isolated from anindividual, then the co-culture of the transfected presenting cells andthe CTLs can lead to release by the CTLs of cytokines, such as IL-2,IFN-γ, or TNF, if the epitope is presented. Higher amounts of releasedTNF will correspond to more efficient processing and presentation of theclass I epitope from the experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis), evolvedsequence. Experimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) antigens that inducecytotoxic T cells that have the capacity to kill infected cells can alsobe identified by measuring the capacity of T cells derived fromimmunized animals to kill infected cells in vitro. Typically the targetcells are first labeled with radioactive isotopes and the release ofradioactivity is an indication of target cell killing after incubationin the presence of T cells from immunized animals. Such cytotoxicityassays are known in the art.

A second method for identifying optimized CTL epitopes does not requirethe isolation of CTLs reacting with the epitope. In this approach, cellsexpressing class I MHC surface glycoproteins are transfected with thelibrary of evolved sequences as above. After suitable incubation toallow for processing and presentation, a detergent soluble extract isprepared from each cell culture and after a partial purification of theMHC-epitope complex (perhaps optional) the products are submitted tomass spectrometry (Henderson et al. (1993) Proc. Nat'l. Acad. Sci. USA90: 10275-10279). Since the sequence is known of the epitope whosepresentation to be increased, one can calibrate the mass spectrogram toidentify this peptide. In addition, a cellular protein can be used forinternal calibration to obtain a quantitative result; the cellularprotein used for internal calibration could be the MHC molecule itself.Thus one can measure the amount of peptide epitope bound as a proportionof the MHC molecules.

4.0.0. Screening for Optimal Induction of Protective Immunity

Vectors that can Provide Efficient, Protective Immunity are SelectedUsing Lethal Infection Models to Choose Vectors that can Prevent theDisease for Further Rounds of Reassembly (Optionally in Combination withOther Directed Evolution Methods Described Herein) and Selection

To select genetic vaccine vectors that provide efficient protectiveimmunity, one can screen the vector libraries in a test mammal usinglethal infection models, such as Pseudomonas aeruginosa, Salmonellatyphimurium, Escherichia coli, Kiebsiella pneumoniae, Toxoplasma gondii,Plasmodium yoeliii, Herpes simplex, influenza virus (e.g., Influenza Avirus), and Vesicular Steatites Virus. Pools of genetic vaccine vectorsor individual vectors are introduced into the animals intradermally,intramuscularly, intravenously, intratracheally, anally, vaginally,orally, or intraperitoneally and vectors that can prevent the diseaseare chosen for further rounds of reassembly (optionally in combinationwith other directed evolution methods described herein) and selection.

Examples: Anti-IL-4 mAbs or Recombinant IL-12; Recombinant IL-12(Advantage of Latter Model is that Infection Occurs Through Lung, CommonRoute of Human Pathogen Invasion)

As an example, optimal vectors can be screened in mice infected withLeishmania major parasites. When injected into footpads of BALB/c mice,these parasites cause a progressive infection later resulting in adisseminated disease with fatal outcome, which can be prevented byanti-IL-4 mAbs or recombinant IL-12 (Chatelain et al. (1992) J. Immunol.148: 1182-1187). Pools of plasmids can be injected intravenously,intraperitoneally or into footpads of these mice, and pools that canprevent the disease are chosen for further analysis and screened forvectors that can cure existing infections. The size of the footpadswelling can be followed visually providing simple yet precisemonitoring of the disease progression. Mice can be infectedintratracheally with Klebsiella pneumoniae resulting in lethalpneumonia, which can be prevented by recombinant IL-12 (Greenberger etal. (1996) J Immunol. 157: 3006-3012). The advantage of this model isthat the infection occurs through the lung, which is a common route ofhuman pathogen invasion. The vectors can be given to the lung togetherwith the pathogen or they can be administered after symptoms are evidentin order to screen for vectors that can cure established infections.

EXAMPLE Influenza- Provides a Way to Screen for Vectors that ProvideProtection at Very Low Quantities of DNA and/or High VirusConcentrations, and it Also Allows One to Analyze the Levels of AntigenSpecific Abs and CTLs Induced In Vivo

In another example, the genetic vaccines are a mouse vaccination modelfor Influenza A virus. Influenza was one of the first models in whichthe efficacy of genetic vaccines was demonstrated (Ulmer et al. (1993)Science 259: 1745-1749). Several Influenza strains are lethal in miceproviding an easy means to screen for efficacy of genetic vaccines.

For example, Influenza virus strain AIPR/8134, which is availablethrough the American Type Culture Collection (ATCC VR-95), causes lethalinfection, but 100% survival can be obtained when the mice are immunizedwith and influenza hemagglutinin (HA) genetic vaccine (Deck et al.(1997) Vaccine 15: 71-78). This model provides a way to screen forvectors that provide protection at very low quantities of DNA and/orhigh virus concentrations, and it also allows one to analyze the levelsof antigen specific Abs and CTLs induced in vivo.

EXAMPLE Mycobacterium tuberculosis Partial Protection, Requires MajorImprovements

The genetic vaccine vectors can also be analyzed for their capacity toprovide protection against infections by Mycobacterium tuberculosis.This is an example of a situation where genetic vaccines have providedpartial protection, and where major improvements are required.

Identification of Candidate Vectors Followed by More Testing

Once a number of candidate vectors has been identified, these vectorscan be subjected to more detailed analysis in additional models. Testingin other infectious disease models (such as HSV, Mycoplasma pulmonis,RSV and/or rotavirus) will allow identification of vectors that areoptimal in each infectious disease.

Optimal Plasmids from the First Round of Screening are Used as theStarting Material for the Next Round, the Successful Vectors areSequenced and the Corresponding Human Genes are Cloned into GeneticVaccine Vectors which are Characterized In Vitro for their Capacity toInduce Differentiation of a Desired Trait.

In each case, the optimal plasmids from the first round of screening canbe used as the starting material for the next round of reassembly(optionally in combination with other directed evolution methodsdescribed herein), assembly and selection. Vectors that are successfulin animal models are sequenced and the corresponding human genes arecloned into genetic vaccine vectors. These vectors are thencharacterized in vitro for their capacity to induce differentiation ofT_(H)1/T_(H)2 cells, activation of T_(H) cells, cytotoxic T lymphocytesand monocytes/macrophages, or other desired trait. Eventually, the mostpotent vectors, based on in vivo data in mice and comparative in vitrostudies in mice and man, are chosen for human trials, and their capacityto counteract various human infectious diseases is investigated.

Methods for Measuring Immune Parameters that Correlate to ProtectiveImmunity

In addition to determining whether a vector pool provides protectiveimmunity, one can measure immune parameters that correlate to protectiveimmunity, such as induction of specific antibodies (particularly IgG)and induction of specific CTL responses. Spleen cells can be isolatedfrom vaccinated mice and measured for the presence of antigen-specific Tcells and induction of T_(H)1 cytokine synthesis profiles. ELISA andcytoplasmic cytokine staining, combined with flow cytometry, can providesuch information on a single-cell level.

5.0.0. Screening of Genetic Vaccine Vectors that Activate HumanAntigen-Specific Lymphocyte Responses

Isolation of PBMCs or APCs to Screen for Vectors with OptimalImmunostimulatory Properties for the Human Immune System

To screen for vectors with optimal immunostimulatory properties for thehuman immune system, peripheral blood mononuclear cells (PBMCs) orpurified professional antigen-presenting cells (APCs) can be isolatedfrom previously vaccinated or infected individuals or from patients withacute infection with the pathogen of interest.

Genetic Vaccine Vectors Encoding the Antigen for which the Individualshave Specific T Cells can be Transfected into PBMC and Induction of TCell Proliferation and Cytokine Synthesis can be Measured; Also Possibleto Screen for Spontaneous Entry of Genetic Vaccine Vector into APCs

Because these individuals have increased frequencies ofpathogen-specific T cells in circulation, antigens expressed in PBMCs orpurified APCs of these individuals will induce proliferation andcytokine production by antigen-specific CD4+ and CD8+ T cells. Thus,genetic vaccine vectors encoding the antigen for which the individualshave specific T cells can be transfected into PBMC of the individuals,after which induction of T cell proliferation and cytokine synthesis canbe measured. Alternatively, one can screen for spontaneous entry of thegenetic vaccine vector into A-PCs, thus providing a means by which toscreen simultaneously for improved transfection efficiency, improvedexpression of antigen and improved induction of activation of specific Tcells. Vectors with the most potent immunostimulatory properties can bescreened based on their capacity to induce B cell proliferation andimmunoglobulin synthesis. One buffy coat derived from a blood donorcontains PBMC lymphocytes from 0.5 liters of blood, and up to 10⁴ PBMCcan be obtained, enabling very large screening experiments using T cellsfrom one donor.

Making EBV-Transformed B Cell Lines from Healthy Vaccinated Individualsfor Subsequent Experiments

When healthy vaccinated individuals (lab volunteers) are studied, onecan make EBV-transformed B cell lines from these individuals. These celllines can be used as antigen presenting cells in subsequent experimentsusing blood from the same donor; this reduces interassay anddonor-to-donor variation). In addition, one can make antigen-specific Tcell clones, after which genetic vaccines are transfected into EBVtransformed B cells.

Efficiency with which the Transformed B Cells Induce Proliferation ofthe Specific T Cell Clones

The efficiency with which the transformed B cells induce proliferationof the specific T cell clones is then studied. When working withspecific T cell clones, the proliferation and cytokine synthesisresponses are significantly higher than when using total PBMCs, becausethe frequency of antigen-specific T cells among PBMC is very low.

Transfection of Cells in Culture by Libraries of Experimentally Evolved(e.g. by Polynucleotide Reassembly &/or Polynucleotide Site-SaturationMutagenesis) DNA Sequences in Appropriate Expression Vectors can Lead toClass I Epitope Presentation

CTL epitopes can be presented by most cells types since the class Imajor histocompatibility complex (MHC) surface glycoproteins are widelyexpressed. Therefore, transfection of cells in culture by libraries ofexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) DNA sequences in appropriateexpression vectors can lead to class I epitope presentation. If specificCTLs directed to a given epitope have been isolated from an individual,then the co-culture of the transfected presenting cells and the CTLs canlead to release by the CTLs of cytokines, such as IL-2, IFN-γ, or TNFα,if the epitope is presented. Higher amounts of released TNFα willcorrespond to more efficient processing and presentation of the class Iepitope from the experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis), evolvedsequence.

Transfecting Cells Expressing Class I MHC Surface Glycoproteins withLibrary of Evolved Sequences, Preparing a Detergent Soluble Extract,Performing a Partial Purification of the MHC-Epitope Complex, and thenSubmitting the Products to Mass Spectrometry

A second method for identifying optimized CTL epitopes does not requirethe isolation of CTLs reacting with the epitope. In this approach, cellsexpressing class I MHC surface glycoproteins are transfected with thelibrary of evolved sequences as above. After suitable incubation toallow for processing and presentation, a detergent soluble extract isprepared from each cell culture and after a partial purification of theMHC-epitope complex (perhaps optional) the products are submitted tomass spectrometry (Henderson et al. (1993) Proc. Nat'l. Acad. Sci. USA90: 10275-10279). Since the sequence is known of the epitope whosepresentation to be increased, one can calibrate the mass spectrogram toidentify this peptide. In addition, a cellular protein can be used forinternal calibration to obtain a quantitative result; the cellularprotein used for internal calibration could be the MHC molecule itself.Thus one can measure the amount of peptide epitope bound as a proportionof the MHC molecules.

6.0.0. SCID-Human Skin Model for Vaccination Studies

Use of Mouse Models in Vaccine Studies Limited in that the MHC Moleculesin Mice and Man are Substantially Different, Meaning that Proteins andPeptides that Efficiently Induce Protective Immune Responses in Mice donot Necessarily Function in Humans

Successful genetic vaccinations require transfection of the target cellsafter injection of the vector, expression of the desired antigen,processing the antigen in antigen presenting cells, presentation of theantigenic peptides in the context of MHC molecules, recognition of thepeptide/MHC complex by T cell receptors, interactions of T cells with Bcells and professional APCs and induction of specific T cell and B cellresponses. All these events could be differentially regulated in mouseand man. A limitation of mouse models in vaccine studies is the factthat the MHC molecules of mice and man are substantially different.Therefore, proteins and peptides that effectively induce protectiveimmune responses in mice do not necessarily function in humans.

Mouse Models can be Used to Study Human Tissues in Mice In Vivo forStudies of Transfection Efficiency, Transfer Sequences, and GeneExpression Levels

To overcome these limitations mouse models can be used to study humantissues in mice in vivo. Live pieces of human skin are xenotransplantonto the back of immunodeficient mice, such as SCID mice, allowingscreening of the vector libraries for optimal properties in human cellsin vivo. Recursive selection of episomal vectors provides strongselection pressure for vectors that remain episomal, yet provide highlevel of gene expression. These mice provide an excellent model forstudies on transfection efficiency, transfer sequences and geneexpression levels. In addition, antigen presenting cells (APCs) derivedfrom these mice can also be used to assess the level of antigensdelivered to professional APCs, and to study the capacity of these cellsto present antigens and induce activation of antigen-specific CD4+ andCD8+ T cells in vitro. Significantly, although SCID mice have severelydeficient T and B cell components, antigen presenting cells (dendriticcells and monocytes) are relatively normal in these mice.

Rendering Immunocompetent Mice Immunodeficient in Order to AidTransplantation of Human Tissue, Enabling Vaccine Studies in Human SkinXenotransplanted into Mice with Genetically Normal Immune Systems asWell, Due To the Transient Nature of the In Vivo Immunosuppression

In one embodiment of this model system, immunocompetent mice arerendered immunodeficient in order to enable transplantation of humantissue. For example, blocking of CD28 and CD40 pathways promoteslong-term survival of allogeneic skin grafts in mice (Larsen et al.(1996) Nature 381: 434). Because the in vivo immunosuppression istransient, this model also enables vaccine studies in human skinxenotransplanted into mice with genetically normal immune systems.Several methods of blocking CD28-B7 interactions and CD40-CD40 ligandinteractions are known to those of skill in the art, including, forexample, administration of neutralizing anti-B7-1 and B7-2 antibodies,soluble CTLA-4, a soluble form of the extracellular portion of CTLA-4, afusion protein that includes CTLA-4 and an Fc portion of an IgGmolecule, and neutralizing anti-CD40 or anti-CD40 ligand antibodies.Additional methods by which one can improve transient immunosuppressioninclude administration of one or more of the following reagents:cyclosporin A, anti-IL-2 receptor α-chain Ab, soluble IL-2 receptor,IL-10, and combinations thereof.

A model in which SCID-mice transplanted with human skin are injectedwith HLA-matched PBMC can be used to analyze vectors that provide longlasting expression in vivo. In this model, the vectors are injected, ortopically applied, into the human skin.

If the HLA-Matched PBMC Injected into Mice Contains Lymphocytes Specificfor the Vector the Transfected Cells Will be Recognized, and EventuallyDestroyed, by These Vector-Specific Lymphocytes, Providing thePossibility to Screen for Vectors that Efficiently Escape Destruction

Thereafter, HLA-matched PBMC are injected into these mice. If the PBMCcontains lymphocytes specific for the vector, the transfected cells willbe recognized, and eventually destroyed, by these vector-specificlymphocytes. Therefore, this model provides possibilities to screen forvectors that efficiently escape destruction by the immune cells. It hasbeen shown that human PBLs injected into mice with human skintransplants reject the organ, indicating that the CTLs reach the skin inthis model. Obtaining HLA-matching skin and blood is possible (e.g.blood sample and skin graft from a patient undergoing skin removal dueto malignancy, or blood and foreskin from the same infant).

SCIDhu Mouse Model: Additionally, Transplanting Human Skin AllowsStudies on the Efficacy of Genetic Vaccine Vectors Following Injectionto the Skin

An additional model that is suitable for screening as described hereinis the modified SCIDhu mouse model, in which pieces of human fetalthymus, liver and bone marrow are transplanted into SCID mice providingfunctional human immune system in mice (Roncarolo et al. (1996) Semin.Immunol. 8: 207). Functional human B and T cells, and APCs can beobserved in these mice. When additionally human skin is transplanted, itis likely to allow studies on the efficacy of genetic vaccine vectorsfollowing injection into the skin. Cotransplantation of skin is likelyto improve the model because it will provide an additional source ofprofessional APCs.

7.0.0. Mouse Model for Studying the Efficiency of Genetic Vaccines inTransfecting Human Muscle Cells and Inducing Human Immune Responses InVivo

There is a Lack of Suitable In Vivo Models for Studies of the Efficiencyof Genetic Vaccines and the Vast Majority of Studies are Performed onthe Mouse Model, in which it is Sometimes Difficult to Predict Whetherthe Results Obtained Reliably Predict Similar Vaccinations in HumansBecause of the Complexity of Events Occurring after Genetic Vaccination

A lack of suitable in vivo models has hampered studies of the efficiencyof genetic vaccines in inducing antigen expression in human muscle cellsand in inducing specific human immune responses. The vast majority ofstudies on the capacity of genetic vaccines to transfect muscle cellsand to induce specific immune responses in vivo have employed a mousemodel. Because of the complexity of events occurring after geneticvaccination, however, it is sometimes difficult to predict whetherresults obtained in the mouse model reliably predict the outcome ofsimilar vaccinations in humans. The events required in successfulgenetic vaccination include transfection of the cells after delivery ofthe plasmid, expression of the desired antigen, processing the antigenin antigen presenting cells, presentation of the antigenic peptides inthe context of MHC molecules, recognition of the peptide/MHC complex byT cell receptors, interactions of T cells with B cells and professionalantigen presenting cells and finally induction of specific T cell and Bcell responses. All these events are likely to be somewhatdifferentially regulated in mouse and man.

The Invention Provides an In Vivo Model for Human Muscle CellTransfection

Muscle tissue, obtained for example from cadavers, is transplantedsubcutaneously into immunodeficient mice, which can be transplanted withtissues from other species without rejection. This model system isespecially valuable because there is no in vitro culture systemavailable for normal muscle cells. Muscle tissue, obtained for examplefrom cadavers, is transplanted subcutaneously into immunodeficient mice.Immunodeficient mice can be transplanted with tissues from other specieswithout rejection. Mice suitable for xenotransplantations include, butare not limited to, SCID mice, nude mice and mice rendered deficient intheir genes encoding RAG1 or RAG2 genes. SCID mice and RAG deficientmice lack functional T and B cells, and therefore are severelyimmunocompromised and are unable to reject transplanted organs. Previousstudies indicate that these mice can be transplanted with human tissues,such as skin, spleen, liver, thymus or bone, without rejection(Roncarolo et al. (1996) Semin. Immunol. 8: 207). After transplantationof human fetal lymphoid tissues into SCID mice, functional human immunesystem can be demonstrated in these mice, a model generally referred toas SCID-hu mice. When human muscle tissue is transplanted into SCID-humice, one can not only study transfection efficiency and expression ofthe desired antigen, but one can also study induction of specific humanimmune responses induced by genetic vaccines in vivo. In this case,muscle and lymphoid organs from the same donor are used. Fetal musclealso has an advantage in that it contains few mature lymphocytes ofdonor origin decreasing likelihood of graft versus host reaction.

Genetic Vaccine Vectors are Introduced into the Human Muscle Tissue toStudy the Expression of the Antigen of Interest

Once the human muscle tissue is established in the mouse, geneticvaccine vectors are introduced into the human muscle tissue to study theexpression of the antigen of interest. When studying transfectionefficiency only, RAG deficient mice are preferred, because these micenever have mature B or T cells in the circulation, whereas “leakiness”of SCID phenotype has been demonstrated which may cause variation in thetransplantation efficiency.

Model Provides an Efficient Means to Study Gene Expression in HumanMuscle Cells In Vivo, Despite the Limited Survival of the Tissue in Mice

The survival of human muscle tissue in mice is likely to be limited evenin immuno-compromised mice. However, because expression studies can beperformed within one or two days, this model provides an efficient meansto study gene expression in human muscle cells in vivo. A modifiedSCID-hu mouse model with human muscle transplanted into these mice canbe used to study human immune responses in mice in vivo.

8.0.0. Screening for Improved Delivery of Vaccines

Identifying Genetic Vaccine Vectors that are Capable of beingAdministered in a Particular Manner

For certain applications, it is desirable to identify genetic vaccinevectors that are capable of being administered in a particular manner,for example, orally or through the skin. The following screening methodsprovide suitable assays; additional assays are also described herein inconjunction with particular genetic vaccine properties for which theassays are especially suitable.

Screening for Oral Delivery Either In Vitro (Based on Caco-2 Cells) orIn Vivo

Screening for oral delivery can be performed either in vitro or in vivo.An example of an in vitro method is based on Caco-2 (human colonadenocarcinoma) cells which are grown in tissue culture. When grown onsemipermeable filters, these cells spontaneously differentiate intocells that resemble human small intestine epithelium, both structurallyand functionally. Genetic vaccine libraries and/or vectors can be placedon one side of the Caco-2 cell layer, and vectors that are able to movethrough the cell layer are detected on the opposite side of the layer.

Libraries can also be screened for amenability to oral delivery in vivo.For example, a library of vectors can be administered orally, afterwhich target tissues are assayed for presence of vectors. Intestinalepithelium, liver, and the bloodstream are examples of tissues that canbe tested for presence of library members. Vectors that are successfulin reaching the target tissue can be recovered and, if furtherimprovement is desired, used in succeeding rounds of reassembly(optionally in combination with other directed evolution methodsdescribed herein) and selection.

Apparatus which Permits Large Numbers of Vectors to be ScreenedEfficiently and can be Used to Study the Effect of Large Numbers ofAgents In Vivo

For screening a library of genetic vaccine vectors for ability totransfect cells upon injection into skin or muscle, the inventionprovides an apparatus which permits large numbers of vectors to bescreened efficiently. This apparatus is based on 96-well format and isdesigned to transfer small volumes (2-5 μl) from a microtiter plate toskin or muscle of laboratory animals, such as mice and rats. Moreover,human muscle or skin transplanted into immunodeficient mice can beinjected.

The apparatus is designed in such a way that the tips move to fit amicrotiter plate. After the reagent of interest has been obtained fromthe plate, the distance of the tips from each other is decreased to 2-3mm, enabling transfer of 96 reagents to an area of 1.6 cm×2.4 cm to 2.4cm×3.6 cm. The volume of each sample transferred is electronicallycontrolled. Each reagent is mixed with a marker agent or dye to enablerecognition of injection site in the tissue. For example, gold particlesof different sizes and shapes are mixed with the reagent of interest,and microscopy and immunohistochemistry can be used to identify eachinjection site and to study the reaction induced by each reagent. Whenmuscle tissue is injected the injection site is first revealed bysurgery.

This apparatus can be used to study the effects of large numbers ofagents in vivo. For example, this apparatus can be used to screenefficiency of large numbers of different DNA vaccine vectors totransfect human skin or muscle cells transplanted into immunodeficientmice.

2.5.10. Enhanced Entry of Genetic Vaccine Vectors into Cells

Using Stochastic (e.g. Polynucleotide Shuffling & Interrupted Synthesis)and Non-Stochastic Polynucleotide Reassembly to Efficiently Improve theCapacity of DNA to Enter the Cytoplasm and Subsequently the Nucleus ofHuman Cells

The methods involve subjecting to stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly polynucleotides which are involved in cell entry. Suchpolynucleotides are referred to herein as “transfer sequences” or“transfer modules.” Transfer modules can be obtained which increasetransfer in a cell-specific manner, or which act in a more generalmanner. Because the exact sequences that affect DNA binding and transferare not often known, stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassembly maybe the only efficient method to improve the capacity of DNA to enter thecytoplasm and subsequently the nucleus of human cells.

The Stochastic (e.g. Polynucleotide Shuffling & Interrupted Synthesis)and Non-Stochastic Polynucleotide Reassembly Methods of the InventionProvide Means for Optimizing DNA Sequences and the Three-DimensionalStructure of the Plasmids for Ability to Confer Upon a Vector theAbility to Enter a Cell Even in the Absence of Detailed Information asto the Mechanism by which this Effect is Achieved

The methods involve reassembling (&/or subjecting to one or moredirected evolution methods described herein) at least first and secondforms of a nucleic acid that comprises a transfer sequence. The firstand second forms differ from each other in two or more nucleotides.Suitable substrates include, for example, transcription factor bindingsites, CpG sequences, poly A, C, G, T oligonucleotides,non-stochastically generated nucleic acid building blocks, and randomDNA fragments such as, for example, genomic DNA, from human or othermammalian species. It has been suggested that cell surface proteins,such as the macrophage scavenger receptor, may act as receptors forspecific DNA binding (Pisetsky (1996) Immunity 5: 303). It is not knownwhether these receptors recognize specific DNA sequences or whether theybind DNA in a sequence non-specific manner. However, GGGG tetrads havebeen shown to enhance DNA binding to cell surfaces (Id.). In addition tothe DNA sequence, the three-dimensional structure of the plasmids mayplay a role in the capacity of these plasmids to enter cells. Thestochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly methods of the inventionprovide means for optimizing such sequences for ability to confer upon avector the ability to enter a cell even in the absence of detailedinformation as to the mechanism by which this effect is achieved.

Clonal Isolates of Vectors Bearing Recombinant Segments are Used toInfect Separate Cultures of Cells and the Percentage of Vectors whichEnter Cells is then Determined by, for Example, Counting CellsExpressing a Marker Expressed by the Vectors in the Course ofTransfection

The resulting library of recombinant transfer modules are screened toidentify at least one optimized recombinant transfer module thatenhances the capability of a vector comprising the transfer module toenter a cell of interest. For example, vectors that include arecombinant transfer module can be contacted with a population of cellsunder conditions conducive to entry of the vector into the cells, afterwhich the percentage of cells in the population which contain thenucleic acid vector is determined. Preferably, the vector will contain aselectable or screenable marker to facilitate identification of cellswhich contain the vector. In a preferred embodiment, clonal isolates ofvectors bearing recombinant segments are used to infect separatecultures of cells. The percentage of vectors which enter cells can thenbe determined by, for example, counting cells expressing a markerexpressed by the vectors in the course of transfection.

The Reassembly (&/or One or More Additional Directed Evolution MethodsDescribed Herein) and Rescreening Process can be Repeated as Necessary,Until a Transfer Module that has Sufficient Ability to Enhance Transferis Obtained

Typically, the reassembly (&/or one or more additional directedevolution methods described herein) process is repeated by reassembling(&/or subjecting to one or more directed evolution methods describedherein) at least one optimized transfer sequence with a further form ofthe transfer sequence to produce a further library of recombinanttransfer modules. The further form can be the same or different from thefirst and second forms. The new library is screened to identify at leastone further optimized recombinant vector module that exhibits anenhancement of the ability of a genetic vaccine vector that includes theoptimized transfer module to enter a cell of interest.

The reassembly (&/or one or more additional directed evolution methodsdescribed herein) and rescreening process can be repeated as necessary,until a transfer module that has sufficient ability to enhance transferis obtained. After one or more of reassembly (&/or one or moreadditional directed evolution methods described herein) and screening,vector modules are obtained which are capable of conferring upon anucleic acid vector the ability to enter at least about 50 percent moretarget cells than a control vector which does not contain the optimizedmodule, more preferably at least about 75 percent more, and mostpreferably at least about 95 or 99 percent more target cells than acontrol vector.

For Integration by Homologous Recombination, Important Factors are theDegree and Length of Homology to Chromosomal Sequences, the Frequency ofSuch Sequences in the Genome, and the Specific Sequence MediatingHomologous Recombination; for Nonhomologous, Illegitimate andSite-Specific Recombination, Recombination is Mediated by Specific Siteson the Therapy Vector which Interact with Cell Encoded RecombinationProteins

Although for vaccine purposes non-integrating vectors are generallypreferred, for some applications it may be desirable to use anintegrating vector; for these applications DNA sequences that directlyor indirectly affect the efficiency of integration can be included inthe genetic vaccine vector. For integration by homologous recombination,important factors are the degree and length of homology to chromosomalsequences, as well as the frequency of such sequences in the genome(e.g., Alu repeats). The specific sequence mediating homologousrecombination is also important, since integration occurs much moreeasily in transcriptionally active DNA. Methods and materials forconstructing homologous targeting constructs are described by e.g.,Mansour (1988) Nature 336:348; Bradley (1992) Bio/Technology 10:534. Fornonhomologous, illegitimate and site-specific recombination,recombination is mediated by specific sites on the therapy vector whichinteract with cell encoded recombination proteins, e.g., Cre/Lox andFIp/Frt systems. See, e.g., Baubonis (1993) Nucleic Acids Res.21:2025-2029, which reports that a vector including a LoxP site becomesintegrated at a LoxP site in chromosomal DNA in the presence of Crerecombinase enzyme.

1.0. Optimization of Genetic Vaccine Components

Optimizing Properties that can Influence the Efficacy of a GeneticVaccine in Modulating an Immune Response in a Mammalian System

Many factors can influence the efficacy of a genetic vaccine inmodulating an immune response. The ability of the vector to enter acell, for example, has a significant effect on the ability of the vectorto modulate an immune response. The strength of an immune response isalso mediated by the immunogenicity of an antigen expressed by a geneticvaccine vector and the level at which the antigen is expressed. Thepresence or absence of costimulatory molecules produced by the geneticvaccine vector can affect not only the strength, but also the type ofimmune response that arises due to introduction of the vector into amammal. An increase in the persistence of a vector in an organism canlengthen the time of immunomodulation, and also makes feasibleself-boosting vectors which do not require multiple administrations toachieve long-lasting protection. The present invention provides methodsfor optimizing many of these properties, thus resulting in geneticvaccine vectors that exhibit improved ability to elicit the desiredeffect on a mammalian immune system.

The Selection from Large Libraries Using Recursive Cycles of Reassembly(Optionally in Combination with Other Directed Evolution MethodsDescribed Herein) to Maximally Access all the Fortuitous but ComplexMechanisms that Cannot be Approached Rationally

Genetic vaccines can contain a variety of functional components, whosepreferred sequences are best determined by stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly, the empirical sequence evolution described indetail herein. The methods of the invention involve, in general,constructing a separate library for each of the major vector componentsby stochastic (e.g. polynucleotide shuffling & interrupted synthesis)and non-stochastic polynucleotide reassembly of multiple homologousstarting sequences, or other methods of generating a population ofrecombinants, resulting in a complex mixture of chimeric sequences. Thebest sequences are selected from these libraries using thehigh-throughput assays described below. After one or more cycles ofselection from each of the single module libraries, the pools of thebest sequences of different modules can be combined by stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly as long as the screens are compatible. Thescreens for promoter, enhancer, intron, transfer sequences, mammalianori, bacterial ori and bacterial marker, and the like, can eventually becombined, resulting in co-optimization of the context of each sequence.An important aspect in these experiments is the selection from largelibraries using recursive cycles of reassembly (optionally incombination with other directed evolution methods described herein) tomaximally access all the fortuitous but complex mechanisms that cannotbe approached rationally, such as DNA transfer into the cell.

A Library of Different Vectors can be Generated by Assembling VectorModules that Provide Promoters, Cytokines, Cytokine Antagonists,Chemokines, Immunostimulatory Sequences, and Costimulatory MoleculesUsing Assembly PCR and Combinatorial Molecular Biology

Assembly PCR is a method for assembly of long DNA sequences, such asgenes, non-stochastically generated nucleic acid building blocks, andfragments of plasmids. In contrast to PCR, there is no distinctionbetween primers and template, because the non-stochastically generatednucleic acid building blocks &/or fragments to be assembled prime eachother. The library of vector modules obtained as described herein can befused with promoters, which can themselves be optimized by thestochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly methods of the invention. Theresulting genes can be assembled combinatorially into DNA vaccinevectors, where each gene is expressed under a different promoter (e.g.,a promoter derived from a library of experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) CMV promoters), and the vector library is screened asdescribed herein to identify vectors which exhibit the desired effect onthe immune system.

Properties that Influence the Efficacy or Desirability of the Vaccine

The methods of the invention are useful for obtaining genetic vaccinesthat are optimized for one or more of many properties that influence theefficacy or desirability of the vaccine. These properties include, butare not limited to, the following.

0.0.0. Episomal Vector Maintenance

Episomally Replicating Vectors are Maintained in a Cell for a LongerPeriod of Time and Permit the Development of Self-Boosting Vaccines

One property that one can optimize using the sequence reassembly methodsof the invention is the ability of a genetic vaccine vector to replicateepisomally in a mammalian cell. Episomal replication of a vaccine vectoris advantageous in many situations. For example, episomally replicatingvectors are maintained in a cell for a longer period of time thannon-replicating vectors, thus resulting in an increased length of immuneresponse modulation or increased delivery of a therapeutically usefulprotein. Episomal replication also permits the development ofself-boosting vaccines which, unlike traditional vaccines, do notrequire multiple vaccine administrations. For example, a self-boostingvaccine vector can include an antigen-encoding gene which is under thecontrol of an inducible control element which allows induction ofantigen expression, and the corresponding immune response, in responseto a specific stimulus. However, screening for naturally occurringvector modules which result in enhanced episomal maintenance usingtraditional approaches or attempts to rationally design mutants withimproved properties would require many person-years of research. Theinvention provides methods for generating and screening orders ofmagnitude more diversity in a short time period.

Using Stochastic (e.g. Polynucleotide Shuffling & Interrupted Synthesis)and Non-Stochastic Polynucleotide Reassembly to Recombine at Least TwoForms of a Nucleic Acid which is Capable of Conferring Upon a GeneticVector the Ability to Replicate Autonomously in Mammalian Cells

The ability of a genetic vaccine vector to replicate episomally can beoptimized by using stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassembly torecombine at least two forms of a nucleic acid which is capable ofconferring upon a genetic vector the ability to replicate autonomouslyin mammalian cells. The two or more forms of the episomal replicationvector module differ from each other in two or more nucleotides. Alibrary of recombinant episomal replication vector modules is produced,and the library is screened to identify one or more optimizedreplication vector modules which, when placed in a genetic vaccinevector, confer upon the vector an enhanced ability to replicateautonomously compared to a vector which contains a non-optimizedepisomal replication vector module.

Repetition of the Stochastic (e.g. Polynucleotide Shuffling &Interrupted Synthesis) and Non-Stochastic Polynucleotide ReassemblyProcess at Least Once to Identify Modules which Exhibit Enhanced Abilityto Confer Episomal Maintenance Upon a Vector Containing the Module

In one embodiment, the stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassemblyprocess is repeated at least once using as a substrate an optimizedepisomal replication vector module obtained from a previous round ofstochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly. The optimized vector moduleobtained in the earlier round is reassembled (&/or subjected to one ormore directed evolution methods described herein) with a further form ofthe vector module, which can be the same as one of the forms used in theearlier round, or can be a different form of a nucleic acid thatfunctions as an episomal replication element. Again, a library ofrecombinant episomal replication vector modules is produced, and thescreening process is repeated to identify those episomal replicationmodules which exhibit enhanced ability to confer episomal maintenanceupon a vector containing the module.

Ability to Replicate Autonomously in Eukaryotic Cells—Examples

Nucleic acids which are useful as substrates for the use of stochastic(e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly to optimize episomalreplication ability include any nucleic acid that is involved inconferring upon a vector the ability to replicate autonomously ineukaryotic cells. For example, papillomavirus sequences E1 and E2,simian virus 40 (SV40) origin of replication, and the like.

Genes from Human Papillomaviruses are Exemplary Episomal ReplicationVector Modules

Exemplary episomal replication vector modules that can be optimizedusing the methods of the invention are genes from human papillomaviruses(HPV) which are involved in episomal replication. HPV arenon-tumorigenic viruses which replicate episomally in skin and arestably expressed in vivo for years. Bernard and Apt (1994) Arch.Dermatol. 130: 210.

Increased Episomal Maintenance of the HPV Genes Involved in EpisomalReplication Using Directed Evolution

Despite these in vivo properties, it has not been possible to maintainHPV episomally in tissue culture due to under replication. The inventionprovides methods by which HPV genes involved in episomal maintenance canbe optimized for use in genetic vaccine vectors. HPV genes involved inepisomal replication include, for example, the E1 and E2 genes. Thus,according to one embodiment of the invention, either or both of the HPVE1 and E2 genes are subjected to stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly to obtain a recombinant episomal replication module which,when placed in a nucleic acid vaccine vector, results in increasedmaintenance of the vector in mammalian cells. In a preferred embodiment,the HPV E1 and E2 genes from different, but closely related, benign HPVsare used in a polynucleotide reassembly procedure, as shown, described&/or referenced herein (including incorporated by reference). Forexample, polynucleotide shuffling of HPV E1 and E2 genes from closelyrelated strains of HPV (such as, for example, HPV 2, 27, and 57) can beused to obtain a library of recombinant E1 and E2 genes which are thensubjected to an appropriate screening method to identify those thatexhibit improved episomal maintenance properties.

Identification, Selection, Enrichment of Recombinant EpisomalReplication Vector Modules that Exhibit Improved Ability to MediateEpisomal Maintenance

To identify recombinant episomal replication vector modules that exhibitimproved ability to mediate episomal maintenance, members of the libraryof recombinant vector modules are inserted into vectors which areintroduced into mammalian cells. The cells are propagated for at leastseveral generations, after which cells that have maintained the vectorare identified. Identification can be accomplished, for example,employing a vector that includes a selectable marker. Cells containingthe library members are propagated in the absence of selection for theselectable marker for at least several generations, after whichselective pressure is added. Cells which survive selection are enrichedfor cells that harbor vectors which contain a recombinant vector modulewhich enhances the ability of the vector to replicate episomally. DNA isrecovered from the selected cells and introduced into bacterial hostcells, allowing recovery of episomal, non-integrated vectors.

Screening by Introducing to a Vector Containing a PolynucleotideEncoding an Antigen that is Present on the Surface of the Cell whenExpressed

In another embodiment of the invention, the screening step isaccomplished by introducing members of the library of recombinantepisomal replication vector modules into a vector that includes apolynucleotide that encodes an antigen which, when expressed, is presenton the surface of a cell. The library of vectors is introduced intomammalian cells which are propagated for at least several generations,after which cells which display the cell surface antigen on the surfaceof the cell are identified. Such cells most likely harbor a geneticvaccine vector which enhances the ability of the vector to replicateautonomously.

Use of Optimized Recombinant Episomal Replication Vector Module toConstruct Genetic Vaccine Vectors

Upon identifying cells which contain an episomally maintained vector,the optimized recombinant episomal replication vector module is obtainedand used to construct genetic vaccine vectors. Cell surface antigenswhich are suitable for use in the screening methods are described above,and others are known to those of skill in the art. Preferably, anantigen is used for which a convenient means of detection is available.

Preferred Cells for Use in the Screening Methods

Cells which are suitable for use in the screening methods include bothcultured mammalian cells and cells which are present in an animal. Toscreen for recombinant vector modules that are intended for use inhumans, the preferred cells for screening purposes are human cells.Generally, initial screening is accomplished in cell culture, whereprocessing of large libraries of experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) material is feasible. In a preferred embodiment, cellswhich display a vector-encoded cell surface antigen on the cell surfaceare identified by flow cytometry based cell sorting methods, such asfluorescence activated cell sorting. This approach allows very largenumbers (>10⁷) cells to be evaluated in a single vial experiment.

Further Testing for Durability In Vivo in an Animal Model

Constructs which replicate autonomously in cell culture and give rise tostrong marker gene expression can be further tested for durability invivo in an animal model. For example, mouse models for studies of humantissues in mice in vivo are described herein. Live pieces of human skinare xenotransplanted onto the back of SCID mice, allowing screening ofthe vector libraries for optimal properties in human cells in vivo.Recursive selection of episomal vectors will provide strong selectionpressure for vectors that remain episomal, yet provide high level ofgene expression.

Introducing a Genetic Vaccine Vector into a Mammal that has a FunctionalHuman Immune System and Testing for the Existence of an Immune ResponseAgainst the Antigen

In another embodiment, the screening step involves introducing a geneticvaccine vector which includes the recombinant episomal replicationvector module, as well as polynucleotide that encodes an antigen orpharmaceutically useful protein, into a mammal that has a functionalhuman immune system. The animal is then tested for the existence of animmune response against the antigen. In a preferred embodiment, themammals used for such assays are non-human mammals that have afunctional human immune system. For example, a functional human immunesystem can be created in an immunodeficient mouse by introducing one ormore of a human fetal tissue selected from the group consisting ofliver, thymus, and bone marrow (Roncarolo et al. (1996) Semin. Immunol.8: 207).

Episomally Maintained Vectors Result in High Signal-to-Noise Ratios UponFACS Selection and Significantly Improve the Possibility to Recover thePlasmids from a Small Number of Selected Cells

Stable episomal vectors which are obtained using the methods of theinvention are useful not only as genetic vaccines, but also are usefultools in other library screening applications. In contrast to randomlyintegrating and transient vectors, episomally maintained vectors resultin high signal-to-noise ratios upon FACS selection, and they alsosignificantly improve the possibility to recover the plasmids from asmall number of selected cells.

1.0.0. Evolution of Optimized Promoters for Expression of an Antigen

Optimizing the Promoter and/or Other Control Sequence to Improve theEfficacy of Genetic Vaccinations, Reduce the Amount of DNA Required forProtective Immunity and Thereby the Cost of Vaccination, Control theType of Cell in which the Gene is Expressed, and/or the Timing of theAntigen Expression

In another embodiment, the invention provides methods of optimizingvector modules such as promoters and other gene expression controlsignals. Usually, a coding sequence for an antigen that is delivered bya genetic vaccine is operably linked to an additional sequence, such asa regulatory sequence, to ensure its expression. These regulatorysequences can include one or more of the following: an enhancer, apromoter, a signal peptide sequence, an intron and/or a polyadenylationsequence. A desirable goal is to increase the level of expression offunctional expression product relative to that achieved withconventional vectors. The efficacy of a genetic vaccine vector oftendepends on the level of expression of an antigen by the vaccine vector.An optimized promoter and/or other control sequence is likely to resultin improved efficacy of genetic vaccinations, reduce the amount of DNArequired for protective immunity and thereby the cost of vaccination.

Moreover, it is sometimes desirable to have control over the type ofcell in which a gene is expressed, and/or the timing of antigenexpression. The methods of the invention provide for optimization ofthese and other factors which are influenced by promoters and othercontrol sequences.

Improving Expression by Increasing the Rate of Production of anExpression Product, Decreasing the Rate of Degradation of the ExpressionProduct, or Improving the Capacity of Expression Product to Perform itsIntended Function Using Stochastic (e.g. Polynucleotide Shuffling &Interrupted Synthesis) and Non-Stochastic Polynucleotide Reassembly ofPolynucleotides Involved in Control of Gene Expression

Improved expression of selection markers can be achieved by performingstochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly, for example. Expression caneffectively be improved by a variety of means, including increasing therate of production of an expression product, decreasing the rate ofdegradation of the expression product or improving the capacity of theexpression product to perform its intended function. The methods involvesubjecting to stochastic (e.g. polynucleotide shuffling & interruptedsynthesis) and non-stochastic polynucleotide reassembly polynucleotideswhich are involved in control of gene expression. At least first andsecond forms of a nucleic acid that comprises a control sequence, whichforms differ from each other in two or more nucleotides, are reassembled(&/or subjected to one or more directed evolution methods describedherein) as described above. The resulting library of recombinanttransfer modules are screened to identify at least one optimizedrecombinant control sequence that exhibits enhanced strength,inducibility, or specificity.

Introduction of the Recombinant Segments at the Level of Fragments(Non-Stochastically Generated &/or Randomly Generated) and In Vitro

The substrates for reassembly (&/or one or more additional directedevolution methods described herein) can be the full-length vectors, orfragments thereof, which include a coding sequence and/or regulatorysequences to which the coding sequence is operably linked. Thesubstrates can include variants of any of the regulatory and/or codingsequence(s) present in the vector. If reassembly (&/or one or moreadditional directed evolution methods described herein) is effected atthe level of fragments, the recombinant segments should be reinsertedinto vectors before screening. If reassembly (&/or one or moreadditional directed evolution methods described herein) proceeds invitro, vectors containing the recombinant segments are usuallyintroduced into cells before screening. An example of a vector suitablefor use in screening of experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis) promotersand other regulatory regions is shown, described &/or referenced herein(including incorporated by reference).

Using an Easily Detected Selection Marker (Green Fluorescent Protein,Cell Surface Protein) when an Additional or Substitute Marker isRequired

Cells containing the recombinant segments can be screened by detectingexpression of the gene encoded by the selection marker. For purposes ofselection and/or screening, a gene product expressed from a vector issometimes an easily detected marker rather than a product having anactual therapeutic purpose, e.g., a green fluorescent protein (see,Crameri (1996) Nature Biotechnol. 14: 315-319) or a cell surfaceprotein. For example, if this marker is green fluorescent protein, cellswith the highest expression levels can be identified by flowcytometry-based cell sorting. If the marker is a cell surface protein,the cells are stained with a reagent having affinity for the protein,such as antibody, and again analyzed by flow cytometry-based cellsorting. However, some genes having a therapeutic purpose, e.g., drugresistance genes, themselves provide a selectable marker, and noadditional or substitute marker is required. Alternatively, the geneproduct can be a fusion protein comprising any combination of detectionand selection markers. Internal reference marker genes can be includedon the vector to detect and compensate for variations in copy number orinsertion site.

Further Round of Reassembly (&/or One or More Additional DirectedEvolution Methods Described Herein) and Screening.

Recombinant segments from the cells showing highest expression of themarker gene can be used as some or all of the substrates in a furtherround of reassembly (&/or one or more additional directed evolutionmethods described herein) and screening, if additional improvement isdesired.

0.0.0.0. Constitutive Promoters

Evolving Control Sequences (Promoters, Enhancers, Etc.) to Express aGene of Interest at a Higher Level than is a Gene Operably Linked to aNon-Evolved Control Sequences

The invention provides methods of evolving nucleotide sequences that arecapable of directing constitutive expression of a gene of interest whichis operably linked to the control sequence. Typically, the controlsequences, which can include promoters, enhancers, and the like, areevolved so that a gene of interest is expressed at a higher level thanis a gene operably linked to a non-evolved control sequence. To screenfor control sequences which are of increased strength, a recombinantlibrary of control sequences can be introduced into a population ofcells and the level of expression of a detectable marker operably linkedto the control sequences determined. Preferably, the optimized promoteris capable of expressing an operably linked gene at a level that is atleast about 30% greater than that of a control promoter construct, morepreferably the optimized promoter is at least about 50% stronger than acontrol, and most preferably at least about 75% or more stronger than acontrol promoter.

Using Improved CMV Promoter/Enhancer Elements (SV40 and Sra) to ExpressForeign Genes Both in Animal Models and in Clinical Applications

Examples of promoters which can be used as substrates in the methodsinclude any constitutive promoter that functions in the intended hostcell. The major immediate-early (IE) region transcriptional regulatoryelements, including promoter and enhancer sequences (thepromoter/enhancer region), of cytomegalovirus (CMV) is widely used forregulating transcription in vectors used for gene therapy because it ishighly active in a broad range of cell types. Optimized CMVtranscriptional regulatory elements which direct increased levels ofantigen expression is generated by the recursive reassembly (&/or one ormore additional directed evolution methods described herein) methods ofthe invention, resulting in improved efficacy of gene therapy. As theCMV promoter and enhancer is active in human and animal cells, theimproved CMV promoter/enhancer elements are used to express foreigngenes both in animal models and in clinical applications. Otherconstitutive promoters that are amenable to use in the claimed methodsinclude, for example, promoters from SV40 and SRα, and other promotersknown to those of skill in the art.

Creating a Library of Chimeric Transcriptional Regulatory ElementsThrough Stochastic (e.g. Polynucleotide Shuffling & InterruptedSynthesis) and Non-Stochastic Polynucleotide Reassembly of Wild-TypeSequences from Two or More of the Five Related Strains of CMV, Obtainingthe Promoter, Enhancer and First Intron Sequences of the IE RegionThrough PCR of the CMV Strains

In a preferred embodiment, a library of chimeric transcriptionalregulatory elements is created by stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly of wild-type sequences from two or more of the five relatedstrains of CMV. The promoter, enhancer and first intron sequences of theIE region are obtained by PCR from the CMV strains: human VR-538 strainAD169 (Rowe (1956) Proc. Soc. Exp. Biol. Med. 92:418; human V-977 strainTowne (Plotkin (1975) Infect. Immunol. 12:521-527); rhesus VR-677 strain68-1 (Asher (1969) Bacteriol. Proc. 269:91); vervet VR-706 strain CSG(Black (1963) Proc. Soc. Exp. Biol. Med. 112:601); and, squirrel monkeyVR-1398 strain SqSHV (Rangan (1980) Lab. Animal Sci. 30:532). Thepromoter/enhancer sequences of the human CMV strains are 95% homologous,and share 70% homology with the sequences of the monkey isolates,allowing the use of polynucleotide reassembly (optionally in combinationwith other directed evolution methods described herein) to generate alibrary with great diversity. Following reassembly (optionally incombination with other directed evolution methods described herein), thelibrary is cloned into a plasmid backbone and used to directtranscription of a marker gene in mammalian cells. An internal markerunder the control of a native promoter is typically included in theplasmid vector, which will allow analysis and sorting of cells harboringequal numbers of vectors.

Expression markers, such as green fluorescent protein (GFP) and CD86(also known as B7.2, see Freeman (1993) J Exp. Med. 178:2185, Chen(1994) J Immunol. 152:4929) can also be used. In addition, transfectionof SV40 T antigen-transformed cells can be used to amplify a vectorwhich contains an SV40 origin of replication. The transfected cells arescreened by FACS sorting to identify those which express high levels ofthe marker gene, normalized against the internal marker to account fordifferences in vector copy numbers per cell. If desired, vectorscarrying optimal, recursively reassembled (&/or subjected to one or moredirected evolution methods described herein) promoter sequences arerecovered and subjected to further cycles of reassembly (optionally incombination with other directed evolution methods described herein) andselection.

1.0.0.0. Cell-Specific Promoters

Reducing the Risk of Autoimmune Disorder Following Introduction ofForeign Antigens into Host Cells and Providing for Efficient Inductionof Protective Immunity Through the Expression of Genetic Vaccines inProfessional APCs, Such as Dendritic Cells and Macrophages

One of the safety concerns associated with genetic vaccines has been thepossibility of autoimmune disorders following introduction of foreignantigens into host cells. This risk can be reduced if the pathogenantigen is specifically expressed in professional APCs that express theproper costimulatory molecules. Although it is somewhat debatable whichcells are the most important cells expressing the pathogen antigenfollowing genetic vaccinations, it is likely that professional APCs areinvolved. It has been shown that blood monocytes express antigenfollowing intramuscular injection of genetic vaccine vectors, anddendritic cells derived from lymph nodes of vaccinated animalsefficiently induced antigen-specific T cell activation (C. Bona, TheFirst Gordon Conference on Genetic Vaccines, Plymouth, N.H., Jul. 21,1997). These data, together with previous studies indicating that smallnumber of dendritic cells expressing antigen or antigenic peptides issufficient to induce activation of antigen-specific T cells (Thomas andLipsky, Stem Cells 14: 196, 1996), support the conclusion that geneticvaccines specifically expressed in professional APC, such as dendriticcells and macrophages, are likely to provide efficient induction ofprotective immunity with minimized chance of adverse effects.

Methods for Obtaining Promoters and Enhancers that Induce HighExpression Levels Specifically in Professional APCs, Exploiting NaturalDiversity as a Source of Substrates for Stochastic (e.g. PolynucleotideShuffling & Interrupted Synthesis) and Non-Stochastic PolynucleotideReassembly

The present invention provides methods of obtaining promoters andenhancers that induce high expression levels specifically inprofessional APCs. Previously existing APC-specific vectors did notprovide sufficient expression levels following genetic vaccinations. Themethods involve performing stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassembly asdescribed above using as substrates different forms of a nucleic acidthat comprises an APC-specific promoter or other control signal.Suitable promoters include, for example, the MHC Class II, and theCD11b, CD11c, and CD40 promoters. Natural diversity of the promoters canbe exploited as a highly appropriate source of substrates for thestochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly. For example, genomic DNA frommonkeys, pigs, dogs, cows, cats, rabbits, rats and mice, can beobtained, and the proper sequences obtained by using multiple PCRprimers specific for the most conserved regions based on known sequenceinformation. The selection of the optimal promoters can be done inmonocytic or B cell lines, such as U937, HL60 or Jijoye, usingFACS-sorting. In addition, SV40⁺ cell lines, such as COS-1 and COS-7,can be used to improve the recovery of the plasmids. Further analysiscan be undertaken in human dendritic cells obtained by culturingperipheral blood monocytes in the presence of IL-4 and GM-CSF asdescribed (Chapuis et al. (1997) Eur. J Immunol. 27: 431).

2.0.0.0. Inducible Promoters

Using Stochastic (e.g. Polynucleotide Shuffling & Interrupted Synthesis)and Non-Stochastic Polynucleotide Reassembly of Two Substrates, Such asTetracycline and Hormone Inducible Expression Systems, to Increase theExpression Level and Inducibility In Vivo of the Promoter ControllingTransgene Expression

A particularly desirable property of a genetic vaccines would be anability to induce the promoter controlling transgene expression simplyby taking an innocuous oral drug, resulting in a boost of the immuneresponse. Essential requirements for inducible promoters are lowbase-line expression and strong inducibility. Several promoters withexquisite in vitro regulation exist, but the expression level andinducibility of each is too low to be useable in vivo. The inventionovercame these problems by stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassemblyusing as substrates two or more variants of a nucleic acid thatfunctions as an inducible control sequence. Suitable substrates include,for example, tetracycline and hormone inducible expression systems, andthe like. Hormones that have been used to regulate gene expressioninclude, for example, estrogen, tomoxifen, toremifen and ecdysone(Ramkumar and Adler (1995) Endocrinology 136: 536-542). Libraries ofrecombinant inducible promoters are screened as described above in thepresence and absence of the inducer.

Tetracycline Responsive System Provides Possibilities to Induce and TurnOff Gene Expression (Ecdysone Responsive Element Another Candidate)

The most commonly used inducible gene expression protocol is thetetracycline responsive system, which provides possibilities to bothinduce and turn off gene expression (Gossen and Bujard (1992) Proc.Nat'l. Acad. Sci. USA 89: 5547; Gossen et al. (1995) Science 268: 1766).A repressor gene is located on the plasmid and binds to an operator inthe promoter. Tetracycline or doxycycline modulates the binding abilityof the repressor. Interestingly, four amino acid changes convert therepressor into an activator. In addition to the tetracycline responsivesystem, other candidates for inducible promoter evolution include theecdysone responsive element (No et al., Proc. Nat'l. Acad. Sci. USA93:3346, 1997).

Inducible Promoters Provide a Means by which a Vaccine Dose can beAdministered Subsequent to the Initial Administration Simply byIngestion of a Reagent that Causes Induction of the Inducible Promoter

Inducible promoters such as those obtained using the methods of theinvention are useful in autoboost vaccines. Particularly when combinedwith a stably maintained episomal vector obtained as described above,the inducible promoters provide a means by which a vaccine dose can beadministered subsequent to the initial administration simply byingestion of a reagent that causes induction of the inducible promoter.A flow cytometry-based screening protocol that is suitable foroptimization of inducible promoters is diagrammed herein.

Testing the Functionality of Autoboosting Vaccines in a Mouse Model

The functionality of autoboosting vaccines can be tested in a mousemodel such as that described above. Genetic vaccine vectors are injectedinto the skin of normal mice and into human skin in SCID-human skinmice. A gene encoding hepatitis B surface antigen (HBsAg) or othersurface antigen is incorporated into these vectors enabling directmeasurements of the levels of antigen produced, because HBsAg levels canbe measured in cell culture supernates and in the circulation of themice. The drug inducing the expression of the antigen is given after 1,2, 4 and 6 weeks, and the expression levels of HBsAg are studied.Moreover, the levels of anti-HBsAg antibodies are measured. The mice arealso injected with a vector containing a pathogen antigen discovered byELI, and specific immune responses are followed.

In Vivo Assessment of Functionality of Autoboosting Genetic Vaccines inHuman Immune System Using SCID-Human Skin Model with SCID-hu Mouse Model

Combining the SCID-human skin model with traditional SCID-hu mouse model(Roncarolo et al., Semin. Immunol. 8: 207, 1996) allows the assessmentof functionality of autoboosting genetic vaccines in human immune systemin vivo, and also allows measurements of human Ab responses in vivo.This model can also be used to assess production of HBsAg after oralboosting of novel genetic vaccine vectors harboring the gene encodingHBsAg.

2.6.3. Evolution of Binding Polypeptides that Enhance Specificity andEfficiency of Genetic Vaccines

The present invention also provides methods for obtaining recombinantnucleic acids that encode polypeptides which can enhance the ability ofgenetic vaccines to enter target cells. Although the mechanisms involvedin DNA uptake are not well understood, the methods of the inventionenable one to obtain genetic vaccines that exhibit enhanced entry tocells, and to appropriate cellular compartments.

Enhancing the Efficiency and Specificity of a Genetic Vaccine NucleicAcid Uptake by a Given Cell Type by Coating the Nucleic Acid with anEvolved Protein that Binds to the Genetic Vaccine Nucleic Acid, and isAlso Capable of Binding to the Target Cell

In one embodiment, the invention provides methods of enhancing theefficiency and specificity of a genetic vaccine nucleic acid uptake by agiven cell type by coating the nucleic acid with an evolved protein thatbinds to the genetic vaccine nucleic acid, and is also capable ofbinding to the target cell. The vector can be contacted with the proteinin vitro or in vivo. In the latter situation, the protein is expressedin cells containing the vector, optionally from a coding sequence withinthe vector. The nucleic acid binding proteins to be evolved usually havenucleic acid binding activity but do not necessarily have any knowncapacity to enhance or alter nucleic acid DNA uptake.

Dna Binding Proteins that can be Used in these Methods

DNA binding proteins which can be used in these methods include, but arenot limited to, transcriptional regulators, enzymes involved in DNAreplication (e.g., recA) and reassembly (&/or one or more additionaldirected evolution methods described herein), and proteins that servestructural functions on DNA (e.g., histones, protamines). Other DNAbinding proteins that can be used include the phage 434 repressor, thelambda phage cl and cro repressors, the E. coli CAP protein, myc,proteins with leucine zippers and DNA binding basic domains such as fosand jun; proteins with ‘POU’ domains such as the Drosophila pairedprotein; proteins with domains whose structures depend on metal ionchelation such as Cys₂H is₂ zinc fingers found in TFIIIA, Zn₂(Cys)₆clusters such as those found in yeast Gal4, the Cys₃ His box found inretroviral nucleocapsid proteins, and the Zn₂(Cys)₈ clusters found innuclear hormone receptor-type proteins; the phage P22 Arc and Mntrepressors (see Knight et al. (1989) J Biol. Chem. 264: 3639-3642 andBowie & Sauerk 1989) J Biol. Chem. 264: 7596-7602. RNA binding proteinsare reviewed by Burd & Dreyfuss (1994) Science 265: 615-621, and includeHIV Tat and Rev.

Formats for Performing Reassembly (&/or One or More Additional DirectedEvolution Methods Described Herein)

As in other methods of the invention, evolution of DNA binding proteinstoward acquisition of improved or altered uptake efficiency is effectiveby one or more cycles of reassembly (&/or one or more additionaldirected evolution methods described herein) and screening. The startingsubstrates can be nucleic acid segments encoding natural or inducedvariants of one or nucleic acid binding proteins, such as thosementioned above. The nucleic acid segments can be present in vectors orin isolated form for the reassembly (&/or one or more additionaldirected evolution methods described herein) step. Reassembly (&/or oneor more additional directed volution methods described herein) canproceed through any of the formats described herein.

For screening purposes, the reassembled (&/or subjected to one or moredirected evolution methods described herein) nucleic acid segments aretypically inserted into a vector, if not already present in such avector during the reassembly (&/or one or more additional directedevolution methods described herein) step.

Including Binding Site in Vector for DNA Binding Protein Recognizing aSpecific Binding Site

The vector generally encodes a selective marker capable of beingexpressed in the cell type for which uptake is desired. If the DNAbinding protein being evolved recognizes a specific binding site (e.g.,lacI binding protein recognizes lacO), this binding site can be includedin the vector. Optionally, the vector can contain multiple binding sitesin tandem.

Transforming Vectors Containing Recombinant Segments into Host Cells andLysing Cells Under Mild Conditions that do not Disrupt Binding ofVectors to DNA Binding Proteins

The vectors containing different recombinant segments are transformedinto host cells, usually E. coli, to allow recombinant proteins to beexpressed and bind to the vector encoding their genetic material. Mostcells take up only a single vector and so transformation results in apopulation of cells, most of which contain a single species of vector.After an appropriate period to allow for expression and binding, cellsare lysed under mild conditions that do not disrupt binding of vectorsto DNA binding proteins. For example, a lysis buffer of 35 mM HEPES (pH7.5 with KOH), 0.1 mM EDTA, 100 mM Na glutamate, 5% glycerol, 0.3 mg/mlBSA, 1 mM DTT, and 0.1 mM PMSF) plus lysozyme (0.3-ml at 10 mg/ml) issuitable (see Schatz et al., U.S. Pat. No. 5,338,665). The complexes ofvector and nucleic acid binding protein are then contacted with cells ofthe type for which improved or altered uptake is desired underconditions favoring uptake. Suitable recipient cells include the humancell types that are common targets in DNA vaccination. These cellsinclude muscle cells, monocytes/macrophages, dendritic cells, B cells,Langerhans cells, keratinocytes, and the M-cells of the gut. Cells frommammals including, for example, human, mouse, and monkey can be used forscreening. Both primary cells and cells obtained from cell lines aresuitable.

Recovery of Cells Expressing Marker and Enriching for RecombinantSegments for Further Rounds of Selection

After incubation, cells are plated with selection for expression of theselective marker present in the vector containing the recombinantsegments. Cells expressing the marker are recovered. These cells areenriched for recombinant segments encoding nucleic acid binding proteinsthat enhance uptake of vectors encoding the respective recombinantsegments. The recombinant segments from cells expressing the marker canthen be subjected to a further round of selection. Usually, therecombinant segments are first recovered from cells, e.g., by PCRamplification or by recovery of the entire vectors. The recombinantsegments can then be reassembled (&/or subjected to one or more directedevolution methods described herein) with each other or with othersources of DNA binding protein variants to generate further recombinantsegments. The further recombinant segments are screened in the samemanner as before.

Using Stochastic (e.g. Polynucleotide Shuffling & Interrupted Synthesis)and Non-Stochastic Polynucleotide Reassembly to Evolve, Particularly,the Carboxy- and Amino-Terminal Peptide Extensions of the HistoneProtein, to Increase the Efficiency of DNA Transfer into the Cells

One example of a method to evolve an optimized nucleic acid bindingdomain involves the reassembly (optionally in combination with otherdirected evolution methods described herein) of histone genes.Histone-condensed DNA can result in increased gene transfer into cells.See, e.g., Fritz et al. (1996) Human Gene Therapy 7: 1395-1404. Thus,stochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly can be used to evolve thehistone protein, particularly the carboxy- and amino-terminal peptideextensions, to increase the efficiency of DNA transfer into cells. Inthis approach, the histone is encoded by the DNA to which it will bebound.

Construction of the Histone Library

The histone library can be constructed by, for example, 1) reassembly(optionally in combination with other directed evolution methodsdescribed herein) of many related histone genes from natural diversity,2) addition of random or partially randomized peptide sequences at theN- and C-terminal sequences of the histone, 3) by addition ofpre-selected protein-encoding regions to the N- or C-termini, such aswhole cDNA libraries, nuclear protein ligand libraries, etc. Theseproteins can be partially randomized and linked to the histone by alibrary of linkers.

Starting Substrates for Evolving Nucleic Acid Binding Sites ContainVariant Binding Sites and Recombinant Forms of these Sites are Screenedas a Component of a Vector that Also Encodes a Nucleic Acid BindingProtein

In a variation of the above procedure, a binding site recognized by anucleic acid binding protein can be evolved instead of, or as well as,the nucleic acid binding protein. Nucleic acid binding sites are evolvedby an analogous procedure to nucleic acid binding proteins except thatthe starting substrates contain variant binding sites and recombinantforms of these sites are screened as a component of a vector that alsoencodes a nucleic acid binding protein.

When the Evolved DNA Binding Protein does not have a High Degree ofSequence Specificity and it is Unknown Precisely which Sites of theVector Used in Screening are Bound by the Protein, the Vector shouldInclude all or Most of the Screening Vector Sequences Together withAdditional Sequences Required to Effect Vaccination or Therapy

Evolved nucleic acid segments encoding DNA binding proteins and/orevolved DNA binding sites can be included in genetic vaccine vectors. Ifthe affinity of the DNA binding protein is specific to a known DNAbinding site, it is sufficient to include that binding site and thesequence encoding the DNA binding protein in the genetic vaccine vectortogether with such other coding and regulatory sequences are required toeffect gene therapy. In some instances, the evolved DNA binding proteinmay not have a high degree of sequence specificity and it may be unknownprecisely which sites on the vector used in screening are bound by theprotein. In these circumstances, the vector should include all or mostof the screening vector sequences together with additional sequencesrequired to effect vaccination or therapy. An exemplary selection schemewhich employs M13 protein VIII is shown, described &/or referencedherein (including incorporated by reference).

Target Cells of Interest

Target cells of interest include, for example, muscle cells, monocytes,dendritic cells, B cells, Langerhans cells, keratinocytes, M-cells ofthe gut, and the like. Cell-specific ligands that are suitable for usewith each of the cell types are known to those of skill in the art. Forexample, suitable proteins to direct binding to antigen presenting cellsinclude CD2, CD28, CTLA-4, CD40 ligand, fibrinogen, factor X, ICAM-1,β-glycan (zymosan), and the Fc portion of immunoglobulin G (Weir'sHandbook of Experimental Immunology, Eds. L. A. Herzenberg, D. M. Weir,L. A. Herzenberg, C. Blackwell, 5th edition, volume IV, chapters 156 and174) because their respective ligands are present on APCs, includingdendritic cells, monocytes/macrophages, B cells, and Langerhans cells.Bacterial enterotoxins or subunits thereof are also of interest fortargeting purposes.

LPS Facilitates the Interaction Between Vector and Monocytes and is AlsoLikely to Act as an Adjuvant, Further Potentiating the Immune Responses

The ability of the vectors to enter and activate APC, such as monocytes,can also be enhanced by coating the vectors with small quantities oflipopolysaccharide (LPS).

This facilitates the interaction between vector and monocytes, whichhave a cell surface receptor for LPS. Due to its immunostimulatoryactivities, LPS is also likely to act as an adjuvant, thereby furtherpotentiating the immune responses.

Receptor Binding Components of Enterotoxins can be Evolved for ImprovedAttachment to Cell Surface Receptors, Improved Entry to and TransportAcross the Cells of the Intestinal Epithelium, and Improved Binding to,and Activation of, B Cells or Other APCs

Enterotoxins produced by certain pathogenic bacteria are useful asagents that bind cells and thus enhance delivery of vaccines, antigens,gene therapy vectors and pharmaceutical proteins. In an exemplaryembodiment of the invention, receptor binding components of enterotoxinsderived from Vibrio cholerae and enterotoxigenic strains of E. coli areevolved for improved attachment to cell surface receptors and forimproved entry to and transport across the cells of the intestinalepithelium. In addition, they can be evolved for improved binding to,and activation of, B cells or other APCs. An antigen of interest can befused to these toxin subunits to illustrate the feasibility of theapproach in oral delivery of proteins and to facilitate the screening ofevolved enterotoxin subunits. Examples of such antigens include growthhormone, insulin, myelin basic protein, collagen and viral envelopeproteins.

Vectors that Contain the Library of Recombinant Enterotoxin BindingMoiety Nucleic Acids are Transfected into a Population of Host Cells,Wherein the Recombinant Enterotoxin Binding Moiety Nucleic Acids areExpressed to Form Recombinant Enterotoxin Binding Moiety Polypeptides

These methods involve reassembling (&/or subjecting to one or moredirected evolution methods described herein) at least first and secondforms of a nucleic acid which comprises a polynucleotide that encodes apreferably non-toxic receptor binding moiety of an enterotoxin. Thefirst and second forms differ from each other in two or morenucleotides, so the stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassemblyresults in production of a library of recombinant enterotoxin bindingmoiety nucleic acids. Suitable enterotoxins include, for example, a V.cholerae enterotoxin, enterotoxins from enterotoxigenic strains of E.coli, salmonella toxin, shigella toxin and campylobacter toxin. Vectorsthat contain the library of recombinant enterotoxin binding moietynucleic acids are transfected into a population of host cells, whereinthe recombinant enterotoxin binding moiety nucleic acids are expressedto form recombinant enterotoxin binding moiety polypeptides. In apreferred embodiment, the recombinant enterotoxin binding moietypolypeptides are expressed as fusion proteins on the surface ofbacteriophage particles. The recombinant enterotoxin binding moietypolypeptides can be screened by contacting the library with a cellsurface receptor of a target cell and determining which recombinantenterotoxin binding moiety polypeptides exhibit enhanced ability to bindto the target cell receptor. The cell surface receptor can be present onthe surface of a target cell itself, or can be attached to a differentcell, or binding can be tested using cell surface receptor that is notassociated with a cell. Examples of suitable cell surface receptorsinclude, for example, G_(m1). Similarly, one can evolve bacterialsuperantigens for altered (increased or decreased) binding to T cellreceptor and MHC class H molecules. These superantigens activate T cellsin an antigen nonspecific manner.

Superantigens binding to T cell receptor/MHC class II molecules includeStaphylococcal enterotoxin B, Urtica dioica superantigen (Musette et al.(1996) Eur. J Immunol. 26:618-22) and Staphylococcal enterotoxin A(Bavari et al. (1996) J Infect. Dis. 174:338-45). Phage display has beenshown to be effective when selecting superantigens that bind MHC class Hmolecules (Wung and Gascoigne (1997) J Immunol. Methods. 204:33-41).

Both CT and CT-B have been Shown to have Potent Adjuvant Activities InVivo and they Enhance Immune Responses after Oral Delivery of Antigensand Vaccines

Cholera toxin (CT) is an oligomeric protein of 84,000 daltons whichconsists of one toxic A subunit (CT-A) covalently linked to five Bsubunits (CT-B). CT-B functions as the receptor binding component andbinds to G_(M1), ganglioside receptors on mammalian cell surfaces. Thetoxic A-subunit is not necessary for the function of CT, and in theabsence of CT-A, functional CT-B pentamers can form (Lebens andHolingren (1994) Dev. Biol. Stand. 82: 215-227). Both CT and CT-B havebeen shown to have potent adjuvant activities in vivo and they enhanceimmune responses after oral delivery of antigens and vaccines(Czerkinsky et al. (1996) Ann. NY Acad. Sci. 778: 185-93; Van Cott etal. (1996) Vaccine 14: 392-8). Moreover, a single dose of CT-Bconjugated to myelin basic protein prevented onset of autoimmuneencephalomyelitis (EAE), a murine model of multiple sclerosis(Czerkinsky et al., supra.). Furthermore, feeding animals with myelinbasic protein conjugated to CT-B after the onset of clinical symptoms (7days) attenuated the symptoms in these animals. Other bacterial toxins,such as enterotoxins of E. coli, Salmonella toxin, Shigella toxin andCampylobacter toxin, have structural similarities with CT. Enterotoxinsof E. coli have the same A-B structure as CT and they also have sequencehomology and share functional similarities.

Family Stochastic (e.g. Polynucleotide Shuffling & InterruptedSynthesis) and Non-Stochastic Polynucleotide Reassembly is FeasibleAmong Enterotoxin-Encoding Nucleic Acids from Different BacterialSpecies

Bacterial enterotoxins can be evolved for improved affinity and entry tocells by polynucleotide (e.g. gene, promoter, enhancer, intron, & thelike) reassembly (optionally in combination with other directedevolution methods described herein). The similarity of E. coli-derivedenterotoxin subunit and CT-B is 78%, and several completely conservedregions of more than eight nucleotides can be found. B subunits from twodifferent strains of E. coli are 98% homologous both at sequence andprotein levels. Thus, family stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassembly isfeasible among enterotoxin-encoding nucleic acids from differentbacterial species.

Screen the Secretion of Chimeric Proteins by V. cholerae by Culturingthe Bacteria in Agar in the Presence of Monoclonal Antibodies Specificfor the Antigen that was Fused to the Toxins

The libraries of experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis) toxinsubunits can be expressed in a suitable host cell, such as V. cholerae.For safety reasons, strains in which the toxic CT-A is deleted arepreferred. An antigen of interest can be fused to the receptor-bindingsubunit. Secretion of chimeric proteins by V. cholerae can be screenedby culturing the bacteria in agar in the presence of monoclonalantibodies specific for the antigen that was fused to the toxins and thelevel of secretion is detected as immunoprecipitation in the agar aroundthe colonies.

Evolving for Improved Binding to the G_(M1), Ganglioside Receptor andOther Receptors, Detecting Binding Between Receptor and Chimeric FusionProteins with a Monoclonal Antibody Specific for the Antigen that wasFused to the Toxin

One can also add G_(M1), ganglioside receptors to the agar in order todetect colonies secreting functional enterotoxin subunits. Coloniesproducing significant levels of the fusion protein are then cultured in96-well plates, and the culture medium is tested for the presence ofmolecules capable of binding to cells or receptors in solution. Bindingof chimeric fusion proteins to G_(M1), ganglioside receptors on cellsurface or in solution can be detected by a monoclonal antibody specificfor the antigen that was fused to the toxin. The assay using whole cellshas the advantage that one may evolve for improved binding also toreceptors other than the G_(M1), ganglioside receptor. When increasingconcentrations of wild-type enterotoxins are added to these assays, onecan detect mutants that bind to receptors with improved affinities.Affinity and specificity of toxin binding can also be determined bysurface plasmon resonance (Kuziemko et al. (1996) Biochemistry 35:6375-84).

Advantage of Large Scale Production and Avoidance of Problems Associatedwith Expression on Phase in the Bacterial Expression System

The advantage of the bacterial expression system is that the fusionprotein is secreted by bacteria that could potentially be used in largescale production. Moreover, because the fusion protein is in solutionduring selection, possible problems associated with expression on phage(such as bias towards selection of mutants that only function on phage)can be avoided.

In Phage Display Mutants can be Easily Further Selected in In VivoAssays when Screening to Identify Enterotoxins with Improved Affinities

Nevertheless, phage display is useful for screening to identifyenterotoxins with improved affinities. A library of experimentallyevolved (e.g. by polynucleotide reassembly &/or polynucleotidesite-saturation mutagenesis) mutants can be expressed on phage, such asM13, and mutants with improved affinity are selected based on bindingto, for example, G_(M1) ganglioside receptors in solution or on a cellsurface. The advantage of this approach is that the mutants can beeasily further selected in in vivo assays as discussed below. Ascreening approach using fusion to M13 protein VIII is diagrammedherein.

The Recombinant Binding Moiety is Expressed in the Cells and Binds tothe Nucleic Acid Binding Domain to Form a Vector-Binding Moiety Complex

Finally, the resulting evolved enterotoxin can be fused with DNA bindingprotein, and genetic vaccine vectors are coated with this fusionprotein. The stochastic (e.g. polynucleotide shuffling & interruptedsynthesis) and non-stochastic polynucleotide reassembly can be doneeither separately, in which case the two domains are assembled afterreassembly (optionally in combination with other directed evolutionmethods described herein), or in a combined reaction. Reassembly(optionally in combination with other directed evolution methodsdescribed herein) results in production of a library of recombinantbinding moiety nucleic acids which can be screened by transfectingvectors which contain the library, as well as a binding site specificfor the nucleic acid binding domain, into a population of host cells.The binding moiety is expressed in the cells and binds to the nucleicacid binding domain to form a vector-binding moiety complex. Host cellscan then be lysed under conditions that do not disrupt binding of thevector-binding moiety complex.

Optimized Recombinant Binding Moiety Nucleic Acids are Isolated fromCells Containing the Vector

The vector-binding moiety complex can then be contacted with a cell ofinterest, after which cells are identified that contain a vector and theoptimized recombinant binding moiety nucleic acids are isolated from thecells.

Increasing the Number of Copies of Target DNA Taken into Those Cellsthat Initially Take Up the Same DNA (Mammalian Cells)

Another method for obtaining enhanced uptake of a target DNA bymammalian cells is also provided by the invention. Specifically, themethod increases the number of copies of target DNA taken into thosecells that initially take up the same DNA.

Cells that Take Up the Target Molecule of DNA (Cell Surface Expressionof Membrane-Associated DNA Binding Domains) Will Express the Factor andhave Increased Specific Affinity for Target DNA that RemainsExtracellular, while Cells that Did not Take Up DNA Will be at aCompetitive Disadvantage as they Will not Bear the Cell Surface TargetDNA-Specific Binding Domain, which is Required for Specifically MediatedDNA Uptake

The method uses cell surface expression of membrane-associated DNAbinding domains of, for example, transcription factors, that are encodedin the target DNA sequence, which also includes the cognate recognitionsequence for the binding domain. Uptake of one molecule of target DNAinto a cell (by any process, passive uptake, electroporation, osmoticshock, other stress) will lead to transcription of the gene encoding thepolynucleotide binding domain. The gene encoding the binding domain isengineered so that the binding domain is expressed in a membraneanchored form. For example, a hydrophobic stretch of amino acids can beencoded at the carboxyl terminus of the binding domain, thus leading tophospho-inositol-glycan (PIG) conjugation after partial cleavage of thisterminal sequence. This, in turn, leads to trafficking and positioningof the binding domain on the cell surface. The same cells that took upthe first molecule of DNA will express the factor and have increasedspecific affinity for target DNA that remains extracellular. Cells thatdid not take up DNA will be at a competitive disadvantage as they willnot bear the cell surface target DNA-specific binding domain, which isrequired for specifically mediated DNA uptake.

Enhanced binding of the target DNA to the target cell will increase theefficiency of DNA internalization and desired intracellular function.This process represents a positive feedback for increased DNA uptakeinto cells that take up DNA first.

Practical Means for Determining which Transcription Factor orCombination of Factors to Use with any Particular Target DNA

The target DNA, whether a circular or linear plasmid, oligonucleotide,bacterial or mammalian chromosomal fragment, is engineered to bear oneor more copies of a DNA recognition sequence for a mammalian orbacterial transcription factor. Many target sequences will already bearone or more such motifs; these can be identified by sequence analysis.Endogenous motifs recognized by these factors also can be identifiedexperimentally by demonstrating that the target DNA binds to one or moreof a panel of transcription factors in an appropriate assay format. Thisprovides a practical means for determining which factor or combinationof factors to use with any particular target DNA.

Motif(s) in the Case of a Small Oligonucleotide or a DNA Plasmid and inthe Cases where More than One DNA Binding Protein Will be Expressed onthe Cell Surface

In the case of a small oligonucleotide or a DNA plasmid (such as usedfor a DNA vaccine), appropriate motifs can be engineered into thesequence. A particular motif can be engineered in one or more copies, intandem or dispersed in the target sequence. Alternatively, a set ofdifferent motifs can be engineered, in tandem or separated, in caseswhere more than one DNA binding protein will be expressed on the cellsurface.

2.6.4. Evolution of Bacteriophage Vectors

Using Stochastic (e.g. Polynucleotide Shuffling & Interrupted Synthesis)and Non-Stochastic Polynucleotide Reassembly, Phase Genetics and DisplayTechnologies to Rapidly Evolve Highly Novel, Potent, and Generic VaccineVehicles

The invention provides methods of obtaining bacteriophage vectors thatexhibit desirable properties for use as genetic vaccine vectors. Theprinciple behind the approach provided by the invention is to combinethe power of stochastic (e.g. polynucleotide shuffling & interruptedsynthesis) and non-stochastic polynucleotide reassembly with theextraordinary power of bacteriophage genetics and the wealth of recentadvances in phage display technologies to rapidly evolve highly novel,potent, and generic vaccine vehicles.

Methods for Delivery of Antigens from Pathogens to Professional APCs,Maximizing Efficiency Through Increasing the Kinetics and Potency of theImmune Response to the Vaccine

The evolved vaccine vehicles can present antigen either (1) in nativeform on the surface of these APCs for the induction of an antibodyresponse or (2) selectively invade APCs and deliver DNA vaccineconstructs to APCs for intracellular expression, processing andpresentation to CTLs. More efficient methods for delivery of antigensfrom pathogens to professional APCs will increase the kinetics andpotency of the immune response to the vaccine.

Affinity Maturation Process, Essential for the Generation of Antibodieswith Sufficient Affinity to Neutralize Pathogenic Antigens, Occurs inGerminal Centers (Spleen) where Follicular Dendritic Cells PresentProtein Antigens to B Cells and Processed Antigen Fragments to T Cells,Making Efficient Delivery of Antigens to FDCs Essential in Increasingthe Kinetics and Potency of the Immune Response to the ImmunizingAntigen

Genetic vaccine delivery vehicles that are evolved according to themethods of the invention are particularly valuable for the rapidinduction of high affinity antibodies which can effectively neutralizeviral epitopes or pathogenic toxins such as superantigens or choleratoxin. High affinity antibodies are generated by somatic mutation of lowaffinity primary response antibodies. This so-called affinity maturationprocess is essential for the generation of antibodies with sufficientaffinity to neutralize pathogenic antigens. Affinity maturation occursin the spleen in germinal centers where follicular dendritic cells(FDCs), professional antigen presenting cells, present protein antigensto B cells and processed antigen fragments to T cells. Clonallyexpanding B cell populations which have undergone somatic mutation areselected for those mutant B cells expressing antibodies with improvedaffinity for antigen. Thus, efficient delivery of antigen to FDCs willincrease the kinetics and potency of the immune response to theimmunizing antigen. Additionally, processed antigen bound to MHC isrequired to stimulate antigen specific T cells. Genetic vaccines areparticularly efficient at priming class I MHC restricted responses dueto intracellular expression of antigen, with a resultant trafficking ofantigen fragments to the class I MHC pathway. Thus, invasivebacteriophage vectors capable of delivery of genetic vaccine constructsor protein antigens to FDCs are useful.

Preferred Bacteriophage for the Purpose of Evolution are Those that havebeen Genetically Well Characterized and Developed for the Display ofForeign Protein Epitopes (of Special Note was M13 Bacteriophage, a SmallFilamentous Phage which is a Versatile, Highly Evolvable Vehicle forEfficient and Targeted Delivery of Protein or DNA Vaccine Vehicles toCellular Targets of Interest

Any of several bacteriophage can be evolved according to the methods ofthe invention. Preferred bacteriophage for these purposes are those thathave been genetically well characterized and developed for the displayof foreign protein epitopes; these include, for example, lambda, T7, andM13 bacteriophage. The filamentous phage M13 is a particularly preferredvector for use in the methods of the invention. M13 is a smallfilamentous bacteriophage that has been used widely to displaypolypeptide fragments in functional, folded form on the surface ofbacteriophage particles. Polypeptides have been fused to both the geneIII and gene VIII coat proteins for such display purposes. Thus, M13 isa versatile, highly evolvable vehicle for efficient and targeteddelivery of protein or DNA vaccine vehicles to cellular targets ofinterest.

Improvements in Methods (Efficient Delivery of Phase, Homing to APCs,and Invasion of Target Cells Using Experimentally Evolved (e.g. byPolynucleotide Reassembly &/or Polynucleotide Site-SaturationMutagenesis) Bacterial Invasion Proteins) Exemplified for BacteriophageVectors and Applicable to Other Types of Genetic Vaccine Vectors

The following three properties are examples of the type of improvementsthat can be achieved by use of the methods of the invention to evolvebacteriophage genetic vaccine vectors: (1) efficient delivery of phageto the bloodstream by inhalation or oral delivery, (2) efficient homingto APCs, and (3) efficient invasion of target cells using experimentallyevolved (e.g. by polynucleotide reassembly &/or polynucleotidesite-saturation mutagenesis) bacterial invasion proteins. Where M13 isused, fusions can be made to both gene III and gene VIII coat proteinsso that two evolved properties can be combined into a single phageparticle. These studies can be performed in test animals such aslaboratory mice so that the evolved constructs can be rapidlycharacterized with respect to their potency as vaccine vehicles. Evolvedinhalable and/or orally deliverable vehicles and evolved invasins willtranslate directly for use in human cells, while the principlesdeveloped in evolving the ability to home to test animal APCs arereadily transferable to human cells by performing analogous selectionson human APCs. While these methods are exemplified for bacteriophagevectors, the methods are also applicable to other types of geneticvaccine vectors.

2.6.4.1. Evolution of Efficient Delivery of Bacteriophage Vehicles byInhalation or Oral Delivery

Method for the Formulation of Proteins into Inhalable Colloids that canbe Absorbed into the Blood Stream Through the Lung (Preparation Involvedin the Invention)

The invention provides methods for obtaining genetic vaccine vectorsthat are capable of efficient delivery to the bloodstream uponadministration by inhalation or by oral administration. Methods havebeen developed for the formulation of proteins into inhalable colloidsthat can be absorbed into the blood stream through the lung. Themechanisms by which proteins are transported into the blood stream arenot clearly understood, and thus improvements are readily approached byevolutionary methods. Using M13 as an example, the invention involvespreparation of a library of, for example, peptide ligands, adhesionmolecules, bacterial enterotoxins, and randomly fragmented cDNA, whichare fused to gene III, for example, of M13. Libraries of >10¹⁰individual fusions are readily achievable with this technology.

M13 Phage Enters the Blood Stream, can be Recovered and Amplified in E.coli Cells, Pass Through Several Rounds of Enrichment, and be FurtherCharacterized and Evolved by Sequencing and Reassembling (Optionally inCombination with Other Directed Evolution Methods Described Herein) theEntire Phase Genome and Subjecting the Phase to Reiterated Cycles ofDelivery, Recovery, Amplification, and Reassembly (Optionally inCombination with Other Directed Evolution Methods Described Herein)

Screening involves preparation of high titer stocks (preferably >10¹²phage particles) in standard colloidal formulations which are deliveredintranasally to test animals, such as mice. Blood samples are taken overthe course of the ensuing day and circulating phage are amplified in E.coli. It has been established that M13 circulates for long periods inthe blood after injection intravenously, and thus it is reasonable toexpect that phage that successfully enter the blood stream through thelung can be efficiently recovered and amplified E. coli cells. In apreferred embodiment, several rounds of enrichment are applied to theinitial libraries in order to enrich for phage that can efficientlyenter the blood stream when delivered intranasally. Candidate clones aretypically tested individually for their relative efficiency of entry,and the best clones can be further characterized by sequencing toidentify the nature of the fusions that confer efficient delivery (ofparticular interest from the cDNA libraries). Selected clones can befurther evolved and for improved entry by reassembling (optionally incombination with other directed evolution methods described herein) theentire phage genome and subjecting the phage to reiterated cycles ofdelivery, recovery, amplification, and reassembly (optionally incombination with other directed evolution methods described herein).

To Obtain Vaccine Vectors that are Effective when Taken Orally,Recombinant Vectors Prepared Through Reassembly (Optionally inCombination with Other Directed Evolution Methods Described Herein) areAdministered, Surviving, Stable Vectors are Recovered from the Stomach,and Vectors that Efficiently Enter the Bloodstream and/or LymphaticTissue can be Recovered from the Blood/Lymph.

An analogous procedure is used to obtain vaccine vectors that areeffective when delivered orally. A genetic vaccine vector library isprepared by stochastic (e.g. polynucleotide shuffling & interruptedsynthesis) and non-stochastic polynucleotide reassembly. The recombinantvectors are packaged and administered to a test animal. Vectors that arestable in the stomach/intestinal environment are recovered, for example,by recovering surviving vectors from the stomach. Vectors thatefficiently enter the bloodstream and/or lymphatic tissue can beidentified by recovering vectors that reach the blood/lymph. A schematicof this selection method is shown, described &/or referenced herein(including incorporated by reference).

2.6.4.2. Evolution of Bacteriophage Vehicles for Efficient Homing toAPCs

Two Selection Formats: the First Consisting of Enriching the Librariesof Random Peptide Ligands and cDNAs Used in (A) Above for Phage whichSelectively Bind to APCs and Using Either Negative or PositiveSelection; the Second Consists of Injecting Phage LibrariesIntravenously, Collecting Target Organs of Interest, Liberating thePhage by Sonication, Further Amplifying and Enriching.

The invention also provides methods of evolving bacteriophage vectors,as well as other types of genetic vaccine vectors, for efficient homingto professional antigen presenting cells. Libraries of random peptideligands and cDNAs used in (A) above are enriched for phage whichselectively bind to APCs by first negatively selecting for binding tonon-APC cell types, and then positively selecting for binding to APCs.The selections is typically performed by mixing high titer stocks ofphage from the libraries (>10¹² phage particles) with cells (˜10⁷ cellsper selection cycle) and either taking the nonbinding phage (negativeselection) or the binding phage from cell pellets (positive selection).An alternative selection format consists of injecting phage librariesintravenously, allowing the libraries to circulate for several hours,collecting target organs of interest (lymph node, spleen), andliberating the phage by sonication. The positively selected phage can beamplified in E. coli and further rounds of enrichment are performed (3-5rounds) if further optimization is desired. After the chosen number ofrounds, individual phage are characterized for their ability to home tolymphoid organs. The best few candidates can be subjected to furtherevolution through iterated rounds of selection, amplification, andreassembly (optionally in combination with other directed evolutionmethods described herein).

2.6.4.3. Evolution of bacteriophage for invasion of APCs

The methods of the invention are also useful for evolving bacteriophageand other genetic vaccine vehicles for invasion of target cells. Thisopens up the possibility of targeting the class I MHC antigen processingpathways with either internalized protein antigen or antigen expressedby DNA vaccine vehicles carried in by the evolved vector.

Efficient Internalization of Pathogenic Bacteria Through InvasinInteraction with Integrins

Invasins comprise a large family of bacterial proteins which interactwith integrins and promote the efficient internalization of pathogenicbacteria such as Salmonella.

Reassembly (Optionally in Combination with Other Directed EvolutionMethods Described Herein) of Different Forms of Polynucleotides EncodingInvasins, Cloning as Fusions to the M13 Gene VIII Coat Protein Gene,Preparing Libraries and Mixing These Libraries with Target APCs

This embodiment of the invention involves reassembling (optionally incombination with other directed evolution methods described herein)different forms of polynucleotides that encode invasins. For example,two or more genes which encode the invasin family of proteins can beexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis). The experimentally evolved(e.g. by polynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) polynucleotides can be cloned as fusions to the M13 geneVIII coat protein gene, for example, and high titer stock of suchlibraries will be prepared. These libraries of bacteriophage can bemixed with target APCs.

Removing Free Phase and Phase Bound to the Cell Surface

After incubation, the cells are exhaustively washed to remove free phageand phage bound to the surface of the cells can be removed by panningagainst polyclonal anti-M13 antibodies.

Obtaining Successful Phage, Amplifying, Reassembling (Optionally inCombination with other directed evolution methods described herein), andselecting, Characterizing for Relative Invasiveness, Combing with GeneIII Fusions (Encoding Pathogenic Epitopes of Interest) and Testing forRelative Abilities to Induce a CTL Response to the Pathogenic Antigens

The cells are then sonicated, thus releasing phage that havesuccessfully entered the target cells (thus protecting them from thepolyclonal anti-M13 antiserum). These phage can, if desired, beamplified, experimentally evolved (e.g. by polynucleotide reassembly&/or polynucleotide site-saturation mutagenesis), and the selectivecycle will be iteratively applied for, e.g., 3-times. Individual phagefrom the final cycle can then be characterized with respect to theirrelative invasiveness. The best candidates can then be combined withgene III fusions that encode pathogenic epitopes of interest. Thesephage can be injected into mice and tested for their relative abilitiesto induce a CTL response to the pathogenic antigens.

Bacteriophage vaccine vehicles evolved for activity in mice according tothe above methods will establish the principles for the evolution ofsimilar vehicles for potent human vaccines. The ability to induce morerapid and potent CTL and neutralizing antibody responses with suchvehicles is an important new tool for the evolution of improvedcountermeasures against pathogens of interest.

2.6.5. Evolution of Improved Immunomodulatory Sequences

Cytokines can dramatically influence macrophage activation andT_(H)1/T_(H)2 cell differentiation, and thereby the outcome ofinfectious diseases. In addition, recent studies strongly suggest thatDNA itself can act as adjuvant by activating the cells of the immunesystem. Specifically, unmethylated CpG-rich DNA sequences were shown toenhance T_(H)1 cell differentiation, activate cytokine synthesis bymonocytes and induce proliferation of B lymphocytes. The invention thusprovides methods for enhancing the immunomodulatory properties ofgenetic vaccines (a) by evolving the stimulatory properties of DNAitself and (b) by evolving genes encoding cytokines and relatedmolecules that are involved in immune system regulation. These genes arethen used in genetic vaccine vectors.

Of particular interest are IFN-α and IL-12, which skew immune responsestowards a T helper 1 (T_(H)1) cell phenotype and, thereby, improve thehost's capacity to counteract pathogen invasions. Also provided aremethods of obtaining improved immunomodulatory nucleic acids that arecapable of inhibiting or enhancing activation, differentiation, oranergy of antigen-specific T cells. Because of the limited informationabout the structures and mechanisms that regulate these events,molecular breeding C71 techniques of the invention provide much fastersolutions than rational design.

The methods of the invention typically involve the use of stochastic(e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly or other methods to create alibrary of experimentally generated (in vitro &/or in vivo)polynucleotides. The library is then screened to identify experimentallygenerated polynucleotides in the library, when included in a geneticvaccine vector or administered in conjunction with a genetic vaccine,are capable of enhancing or otherwise altering an immune responseinduced by the vector. The screening step, in some embodiments, caninvolve introducing a genetic vaccine vector that includes theexperimentally generated polynucleotides into mammalian cells anddetermining whether the cells, or culture medium obtained by growing thecells, is capable of modulating an immune response.

Optimized recombinant vector modules obtained through polynucleotidereassembly (&/or one or more additional directed evolution methodsdescribed herein) are useful not only as components of genetic vaccinevectors, but also for production of polypeptides, e.g., modifiedcytokines and the like, that can be administered to a mammal to enhanceor shift an immune response. Polynucleotide sequences obtained using thestochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly methods of the invention can beused as a component of a genetic vaccine, or can be used for productionof cytokines and other immunomodulatory polypeptides that are themselvesused as therapeutic or prophylactic reagents. If desired, the sequenceof the optimized immunomodulatory polypeptide-encoding polynucleotidescan be determined and the deduced amino acid sequence used to producepolypeptides using methods known to those of skill in the art.

2.6.5.1 Immunostimulatory DNA Sequences

The invention provides methods of obtaining polynucleotides that areimmunostimulatory when introduced into a mammal. Oligonucleotides thatcontain hexamers with a central CpG flanked by two 5′ purines (GpA orApA) and two 3′ pyrimidines (TpC or TpT) efficiently induce cytokinesynthesis and B cell proliferation (Krieg et al. (1995) Nature 374: 546;Klinman et al. (1996) Proc. Nat'l. Acad. Sci. USA 93: 2879; Pisetsky(1996) Immunity 5: 303-10) in vitro and act as adjuvants in vivo.Genetic vaccine vectors in which immunostimulatory sequence-(ISS)containing oligos are inserted have increased capacity to enhanceantigen-specific antibody responses after DNA vaccination. The minimallength of an ISS oligonucleotide for functional activity in vitro iseight (Klinman et al., supra.). Twenty-mers with three CG motifs werefound to be significantly more efficient in inducing cytokine synthesisthan a 15-mer with two CG motifs (Id.). GGGG tetrads have been suggestedto be involved in binding of DNA to cell surfaces (macrophages expressreceptors, for example scavenger receptors, that bind DNA) (Pisetsky etal., supra.).

According to the invention, a library is generated by subjecting toreassembly (&/or one or more additional directed evolution methodsdescribed herein) random DNA (e.g., fragments of human, murine, or othergenomic DNA), oligonucleotides that contain known ISS, poly A, C, G or Tsequences, or combinations thereof. The DNA, which includes at leastfirst and second forms which differ from each other in two or morenucleotides, are reassembled (&/or subjected to one or more directedevolution methods described herein) to produce a library ofexperimentally generated polynucleotides.

The library is then screened to identify those experimentally generatedpolynucleotides that exhibit immunostimulatory properties. For example,the library can be screened for induction cytokine production in vitroupon introduction of the library into an appropriate cell type. Adiagram of this procedure is shown, described &/or referenced herein(including incorporated by reference). Among the cytokines that can beused as an indicator of immunostimulatory activity are, for example,IL-2, IL-4, IL-5, IL-6, IL-10, IL-12, IL-13, IL-15, and IFN-γ. One canalso test for changes in ratios of IL-4/IFN-K, IL-4/IL-2, IL-5/IFN-γ,IL-5/IL-2, IL-13/IFN-γ, IL-13/IL-2. An alternative screening method isthe determination of the ability to induce proliferation of cellsinvolved in immune responses, such as B cells, T cells,monocytes/macrophages, total PBL, and the like. Other screens includedetecting induction of APC activation based on changes in expressionlevels of surface antigens, such as B7-1 (CD80), B7-2 (CD86), MHC classI and II, and CD14.

Other useful screens include identifying, experimentally generatedpolynucleotides that induce T cell proliferation. Because ISS sequencesinduce B cell activation, and because of several homologies betweensurface antigens expressed by T cells and B cells, polynucleotides canbe obtained that have stimulatory activities on T cells.

Libraries of experimentally generated polynucleotides can also bescreened for improved CTL and antibody responses in vivo and forimproved protection from infection, cancer, allergy or autoimmunity.Experimentally generated polynucleotides that exhibit the desiredproperty can be recovered from the cell and, if further improvement isdesired, the reassembly (optionally in combination with other directedevolution methods described herein) and screening, can be repeated.Optimized ISS sequences can be used as an adjuvant separately from anactual vaccine, or the DNA sequence of interest can be fused to agenetic vaccine vector.

2.6.5.2. Cytokines, Chemokines, and Accessory Molecules

The invention also provides methods for obtaining optimized cytokines,cytokine antagonists, chemokines, and other accessory molecules thatdirect, inhibit, or enhance immune responses. For example, the methodsof the invention can be used to obtain genetic vaccines and otherreagents (e.g., optimized cytokines, and the like) that, whenadministered to a mammal, improve or alter an immune response. Theseoptimized immunomodulators are useful for treating infectious diseases,as well as other conditions such as inflammatory disorders, in anantigen non-specific manner.

For example, the methods of the invention can be used to developoptimized immunomodulatory molecules for treating allergies. Theoptimized immunomodulatory molecules can be used alone or in conjunctionwith antigen-specific genetic vaccines to prevent or treat allergy. Fourbasic mechanisms are available by which one can achieve specificimmunotherapy of allergy. First, one can administer a reagent thatcauses a decrease in allergen-specific T_(H)2 cells. Second, a reagentcan be administered that causes an increase in allergen-specific T_(H)1cells. Third, one can direct an increase in suppressive CD8⁺ T cells.

Finally, allergy can be treated by inducing anergy of allergen-specificT cells. In this example, cytokines are optimized using the methods ofthe invention to obtain reagents that are effective in achieving one ormore of these immunotherapeutic goals. The methods of the invention areused to obtain anti-allergic cytokines that have one or more propertiessuch as improved specific activity, improved secretion afterintroduction into target cells, are effective at a lower dose thannatural cytokines, and fewer side effects. Targets of particularinterest include interferon-α/γ, IL-10, IL-12, and antagonists of IL-4and IL-13.

The optimized immunomodulators, or optimized experimentally generatedpolynucleotides that encode the immunomodulators, can be administeredalone, or in combination with other accessory molecules. Inclusion ofoptimal concentrations of the appropriate molecules can enhance adesired immune response, and/or direct the induction or repression of aparticular type of immune response. The polynucleotides that encode theoptimized molecules can be included in a genetic vaccine vector, or theoptimized molecules encoded by the genes can be administered aspolypeptides.

In the methods of the invention, a library of experimentally generatedpolynucleotides that encode immunomodulators is created by subjectingsubstrate nucleic acids to a reassembly (&/or one or more additionaldirected evolution methods described herein) protocol, such asstochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly or other method known to thoseof skill in the art. The substrate nucleic acids are typically two ormore forms of a nucleic acid that encodes an immunomodulator ofinterest.

Cytokines are among the immunomodulators that can be improved using themethods of the invention. Cytokine synthesis profiles play a crucialrole in the capacity of the host to counteract viral, bacterial andparasitic infections, and cytokines can dramatically influence theefficacy of genetic vaccines and the outcome of infectious diseases.Several cytokines, for example IL-1, IL-2, IL-3, IL-4, IL-S, IL-6, IL-7,IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IL-16, IL-17,IL-18, G-CSF, GM-CSF, IFN-α, IFN-γ, TGF-β, TNF-α, TNF-β, IL-20 (MDA-7),and flt-3 ligand have been shown stimulate immune responses in vitro orin vivo. Immune functions that can be enhanced using appropriatecytokines include, for example, B cell proliferation, Ig synthesis, Igisotype switching, T cell proliferation and cytokine synthesis,differentiation of T_(H)1 and T_(H)2 cells, activation and proliferationof CTLs, activation and cytokine production bymonocytes/macrophages/dendritic cells, and differentiation of dendriticcells from monocytes/macrophages.

In some embodiments, the invention provides methods of obtainingoptimized immunomodulators that can direct an immune response towards aT_(H)1 or a T_(H)2 response. The ability to influence the direction ofimmune responses in this manner is of great importance in development ofgenetic vaccines. Altering the type of TH response can fundamentallychange the outcome of an infectious disease. A high frequency of T_(H)1cells generally protects from lethal infections with intracellularpathogens, whereas a dominant T_(H)2 phenotype often results indisseminated, chronic infections. For example, in human, the T_(H)1phenotype is present in the tuberculoid (resistant) form of leprosy,while the T_(H)2 phenotype is found in lepromatous, multibacillary(susceptible) lesions (Yamamura et al. (1991) Science 254: 277).Late-stage AIDS patients have the T_(H)2 phenotype. Studies in familymembers indicate that survival from meningococcal septicemia depends onthe cytokine synthesis profile of PBL, with high IL-10 synthesis beingassociated with a high risk of lethal outcome and high TNF-α beingassociated with a low risk. Similar examples are found in mice. Forexample, BALB/c mice are susceptible to Leishmania major infection;these mice develop a disseminated fatal disease with a T_(H)2 phenotype.Treatment with anti-IL-4 monoclonal antibodies or with IL-12 induces aT_(H)1 response, resulting in healing. Anti-interferon-γ monoclonalantibodies exacerbate the disease. For some applications, it ispreferable to direct an immune response in the direction of a T_(H)2response.

For example, where increased mucosal immunity is desired, includingprotective immunity, enhancing the T_(H)2 response can lead to increasedantibody production, particularly IgA. T helper (T_(H)) cells areprobably the most important regulators of the immune system. T_(H) cellsare divided into two subsets, based on their cytokine synthesis pattern(Mosmann and Coffman (1989) Adv. Immunol. 46: 111). T_(H)1 cells producehigh levels of the cytokines IL-2 and IFN-γ and no or minimal levels ofIL-4, IL-5 and IL-13. In contrast, T_(H)2 cells produce high levels ofIL-4, IL-5 and IL-13, and IL-2 and IFN-γ production is minimal orabsent. T_(H)1 cells activate macrophages, dendritic cells and augmentthe cytolytic activity of CD8⁺ cytotoxic T lymphocytes and naturalkiller (NK) cells (Paul and Seder (1994) Cell 76: 241), whereas T_(H)2cells provide efficient help for B cells and also mediate allergicresponses due to the capacity of T_(H)2 cells to induce IgE isotypeswitching and differentiation of B cells into IgE secreting cells(Punnonen et al. (1993) Proc. Nat'l. Acad. Sci. USA 90: 3730).

The screening methods for improved cytokines, chemokines, and otheraccessory molecules are generally based on identification of modifiedmolecules that exhibit improved specific activity on target cells thatare sensitive to the respective cytokine, chemokine, or other accessorymolecules. A library of recombinant cytokine, chemokine, or accessorymolecule nucleic acids can be expressed on phage or as purified proteinand tested using in vitro cell culture assays, for example. Importantly,when analyzing the recombinant nucleic acids as components of DNAvaccines, one can identify the most optimal DNA sequences (in additionto the functions of the protein products) in terms of theirimmunostimulatory properties, transfection efficiency, and theircapacity to improve the stabilities of the vectors. The identifiedoptimized recombinant nucleic acids can then be subjected to new roundsof reassembly (optionally in combination with other directed evolutionmethods described herein) and selection.

In one embodiment of the invention, cytokines are evolved that directdifferentiation of T_(H)1 cells. Because of their capacities to skewimmune responses towards a T_(H)1 phenotype, the genes encodinginterferon-α (IFN-α) and interleukin-12 (IL-12) are preferred substratesfor reassembly (&/or one or more additional directed evolution methodsdescribed herein) and selection in order to obtain maximal specificactivity and capacity to act as adjuvants in genetic vaccinations. IFN-αis a particularly preferred target for optimization using the methods ofthe invention because of its effects on the immune system, tumor cellsgrowth and viral replication. Due to these activities, IFN-α a was thefirst cytokine to be used in clinical practice. Today, IFN-α is used fora wide variety of applications, including several types of cancers andviral diseases. IFN-α also efficiently directs differentiation of humanT cells into T_(H)1 phenotype (Parronchi et al. (1992) J Immunol. 149:2977). However, it has not been thoroughly investigated in vaccinationmodels, because, in contrast to human systems, it does not affect T_(H)1differentiation in mice.

The species difference was recently explained by data indicating that,like IL-12, IFN-α a induces STAT4 activation in human cells but not inmurine cells, and STAT4 has been shown to be required in IL-12 mediatedT_(H)1 differentiation (Thierfelder et al. (1996) Nature 382: 171).

Family stochastic (e.g. polynucleotide shuffling & interruptedsynthesis) and non-stochastic polynucleotide reassembly is a preferredmethod for optimizing IFN-α, using as substrates the mammalian IFN-αgenes, which are 85%-97% homologous. Greater 10²⁶ distinct recombinantscan be generated from the natural diversity in these genes. To allowrapid parallel analysis of recombinant interferons, one can employ highthroughput methods for their expression and biological assay as fusionproteins on bacteriophage.

Recombinants with improved potency and selectivity profiles are beingselectively bred for improved activity. Variants which demonstrateimproved binding to IFN-α receptors can be selected for further analysisusing a screen for mutants with optimal capacity to direct T_(H)1differentiation. More specifically, the capacities of IFN-α mutants toinduce IL-2 and IFN-γ production in in vitro human T lymphocyte culturescan be studied by cytokine-specific ELISA and cytoplasmic cytokinestaining and flow cytometry.

IL-12 is perhaps the most potent cytokine that directs T_(H)1 responses,and it has also been shown to act as an adjuvant and enhance T_(H)1responses following genetic vaccinations (Kim et al. (1997) J Immunol.15 8: 816). IL-12 is both structurally and functionally a uniquecytokine. It is the only heterodimeric cytokine known to date, composedof a 35 kD light chain (p35) and a 40 kD heavy chain (p40) (Kobayashi etal (1989) J Exp. Med. 170: 827; Stem et al. (1990) Proc. Nat'l. Acad.Sci. USA 87: 6808).

Recently Lieschke et al. ((1997) Nature Biotech. 15: 3 5) demonstratedthat a fusion between p35 and p40 genes results in a single gene thathas activity comparable to that of the two genes expressed separately.These data indicate that it is possible to reassemble IL-12 genes as oneentity, which is beneficial in designing the reassembly protocol(optionally in combination with other directed evolution methodsdescribed herein). Because of its T cell growth promoting activities,one can use normal human peripheral blood T cells in the selection ofthe most active IL-12 genes, enabling direct selection of IL-12 mutantswith the most potent activities on human T cells. IL-12 mutants can beexpressed in CHO cells, for example, and the ability of the supernatantsto induce T cell proliferation determined. The concentrations of IL-12in the supernatants can be normalized based on a specific ELISA thatdetects a tag fused to the experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) IL-12 molecules.

Incorporation of evolved IFN-α and/or IL-12 genes into genetic vaccinevectors is expected to be safe. The safety of IFN-α has beendemonstrated in numerous clinical studies and in everyday hospitalpractice. A Phase II trial of IL-12 in the treatment of patients withrenal cell cancer resulted in several unexpected adverse effects (Taharaet al. (1995) Human Gene Therapy 6: 1607). However, IL-12 gene as acomponent of genetic vaccines aims at high local expression levels,whereas the levels observed in circulation are minimal compared to thoseobserved after systemic bolus injections. In addition, some of theadverse effects of systemic IL-12 treatments are likely to be related toits unusually long half-life (up to 48 hours in monkeys). Stochastic(e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly may allow selection for ashorter half-life, thereby reducing the toxicity even after high bolusdoses.

In other cases, genetic vaccines that can induce T_(H)2 responses arepreferred, especially when improved antibody production is desired. Asan example, IL-4 has been shown to direct differentiation of T_(H)2cells (which produce high levels of IL-4, IL-5 and IL-13, and mediateallergic immune responses). Immune responses that are skewed towardsT_(H)2 phenotype are preferred when genetic vaccines are used toimmunize against autoimmune diseases prophylactically. T_(H)1 responsesare also preferred when the vaccines are used to treat and modulateexisting autoimmune responses, because autoreactive T cells aregenerally of T_(H)1 phenotype (Liblau et al. (1995) Immunol. Today16:34-38). IL-4 is also the most potent cytokine in induction of IgEsynthesis; IL-4 deficient mice are unable to produce IgE. Asthma andallergies are associated with an increased frequency of IL-4 producingcells, and are genetically linked to the locus encoding IL-4, which ison chromosome 5 (in close proximity to genes encoding IL-3, IL-5, IL-9,IL-13 and GM-CSF). IL-4, which is produced by activated T cells,basophils and mast cells, is a protein that has 153 amino acids and twopotential N-glycosylation sites. Human IL-4 is only approximately 50%identical to mouse IL-4, and IL-4 activity is species-specific. Inhuman, IL-13 has activities similar to those of IL-4, but IL-13 is lesspotent than IL-4 in inducing IgE synthesis. IL-4 is the only cytokineknown to direct T_(H)2 differentiation.

Improved IL-2 agonists are also useful in directing T_(H)2 celldifferentiation, whereas improved IL-4 antagonists can direct T_(H)1cell differentiation. Improved IL-4 agonists and antagonists can begenerated by the reassembly (optionally in combination with otherdirected evolution methods described herein) of IL-4 or soluble IL-4receptor. The IL-4 receptor consists of an IL-4R α-chain (140 kDhigh-affinity binding unit) and an IL-2R γ-chain (these cytokinereceptors share a common K-chain). The IL-4R α-chain is shared by IL-4and IL-13 receptor complexes. Both IL-4 and IL-13 induce phosphorylationof the IL-4R α-chain, but expression of IL-4R α-chain alone ontransfectants is not sufficient to provide a functional IL-4R. SolubleIL-4 receptor currently in clinical trials for the treatment ofallergies. Using the stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassemblymethods of the invention, one can evolve a soluble IL-4 receptor thathas improved affinity for IL-4. Such receptors are useful for thetreatment of asthma and other T_(H)2 cell mediated diseases, such assevere allergies. The reassembly (optionally in combination with otherdirected evolution methods described herein) reactions can takeadvantage of natural diversity present in cDNA libraries from activatedT cells from human and other primates. In a typical embodiment, anexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) IL-4R α-chain library isexpressed on a phage, and mutants that bind to IL-4 with improvedaffinity are identified. The biological activity of the selected mutantsis then assayed using cell-based assays.

IL-2 and IL-15 are also of particular interest for use in geneticvaccines. IL-2 acts as a growth factor for activated B and T cells, andit also modulates the functions of NK-cells. IL-2 is predominantlyproduced by T_(H)1-like T cell clones, and, therefore, it is consideredmainly to function in delayed type hypersensitivity reactions. However,IL-2 also has potent, direct effects on proliferation and Ig-synthesisby B cells. The complex immunoregulatory properties of IL-2 arereflected in the phenotype of IL-2 deficient mice, which have highmortality at young age and multiple defects in their immune functionsincluding spontaneous development of inflammatory bowel disease. IL-15is a more recently identified cytokine produced by multiple cell types.IL-15 shares several, but not all, activities with IL-2. Both IL-2 andIL-15 induce B cell growth and differentiation. However, assuming thatIL-15 production in IL-2 deficient mice is normal, it is clear thatIL-15 cannot substitute for the function of IL-2 in vivo, since thesemice have multiple immunodeficiencies. IL-2 has been shown tosynergistically enhance IL-10-induced human Ig production in thepresence of anti-CD40 mAbs, but it antagonized the effects of IL-4. IL-2also enhances IL-4-dependent IgE synthesis by purified B cells. On theother hand, IL-2 was shown to inhibit IL-4-dependent murine IgG1 and IgEsynthesis both in vitro and in vivo. Similarly, IL-2 inhibitedIL-4-dependent human IgE synthesis by unfractionated human PBMC, but theeffects were less significant than those of IFN-α or IFN-γ. Due to theircapacities to activate both B and T cells, IL-2 and IL-15 are useful invaccinations. In fact, IL-2, as protein and as a component of geneticvaccines, has been shown to improve the efficacy of the vaccinations.Improving the specific activity and/or expression levels/kinetics ofIL-2 and IL-15 through use of the stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly methods of the invention increases the advantageous effectscompared to wild-type IL-2 and IL-15.

Another cytokine of particular interest for optimization and use ingenetic vaccines according to the methods of the invention isinterleukin-6. IL-6 is a monocyte-derived cytokine that was originallydescribed as a B cell differentiation factor or B cell stimulatoryfactor-2 because of its ability to enhance Ig levels secreted byactivated B cells.

IL-6 has also been shown to enhance IL-4-induced IgE synthesis. It hasalso been suggested that IL-6 is an obligatory factor for human IgEsynthesis, because neutralizing anti-IL-6 mAbs completely blockedIL-4-induced IgE synthesis. IL-6 deficient mice have impaired capacityto produce IgA. Because of its potent activities on the differentiationof B cells, IL-6 can enhance the levels of specific antibodies producedfollowing vaccination. It is particularly useful as a component of DNAvaccines because high local concentrations can be achieved, therebyproviding the most potent effects on the cells adjacent to thetransfected cells expressing the immunogenic antigen. IL-6 with improvedspecific activity and/or with improved expression levels, obtained bystochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly, will have more beneficialeffects than the wild-type IL-6.

Interleukin-8 is another example of a cytokine that, when modifiedaccording to the methods of the invention, is useful in geneticvaccines. IL-8 was originally identified as a monocyte-derivedneutrophil chemotactic and activating factor. Subsequently, IL-8 wasalso shown to be chemotactic for T cells and to activate basophilsresulting in enhanced histamine and leukotriene release from thesecells. Furthermore, IL-8 inhibits adhesion of neutrophils tocytokine-activated endothelial cell monolayers, and it protects thesecells from neutrophil-mediated damage. Therefore, endothelial cellderived IL-8 was suggested to attenuate inflammatory events occurring inthe proximity of blood vessel walls. IL-8 also modulates immunoglobulinproduction, and inhibits IL-4-induced IgG4 and IgE synthesis by bothunfractionated human PBMC and purified B cells in vitro. This inhibitoryeffect was independent of IFN-α, IFN-γ or prostaglandin E2. In addition,IL-8 inhibited spontaneous IgE synthesis by PBMC derived from atopicpatients. Due to its capacity to attract inflammatory cells, IL-8, likeother chemotactic agents, is useful in potentiating the functionalproperties of vaccines, including DNA vaccines (acting as an adjuvant).The beneficial effects of IL-8 can be improved by using the stochastic(e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly methods of the invention toobtain IL-8 with improved specific activity and/or with improvedexpression in target cells.

Interleukin-5, and antagonists thereof, can also be optimized using themethods of the invention for use in genetic vaccines. IL-5 is primarilyproduced by T_(H)2-type T cells and appears to play an important role inthe pathogenesis of allergic disorders because of its ability to induceeosinophilia. IL-5 acts as an eosinophil differentiation and survivalfactor in both mouse and man. Blocking IL-5 activity by use ofneutralizing monoclonal antibodies strongly inhibits pulmonaryeosinophilia and hyperactivity in mouse models, and IL-5 deficient micedo not develop eosinophilia. These data also suggest that IL-5antagonists may have therapeutic potential in the treatment of allergiceosinophilia.

IL-5 has also been shown to enhance both proliferation of, and Igsynthesis by, activated mouse and human B cells. However, other studiessuggested that IL-5 has no effect on proliferation of human B cells,whereas it activated eosinophils. IL-5 apparently is not crucial formaturation or differentiation of conventional B cells, because antibodyresponses in IL-5 deficient mice are normal. However, these mice have adevelopmental defect in their CD5⁺ B cells indicating that IL-5 isrequired for normal differentiation of this B cell subset in mice. Atsuboptimal concentrations of IL-4, IL-5 was shown to enhance IgEsynthesis by human B cells in vitro. Furthermore, a recent studysuggested that the effects of IL-5 on human B cells depend on the modeof B cell stimulation. IL-5 significantly enhanced IgM synthesis by Bcells stimulated with Moraxella catarrhalis. In addition, IL-5synergized with suboptimal concentrations of IL-2, but had no effect onIg synthesis by SAC-activated B cells. Activated human B cells alsoexpressed IL-5 mRNA suggesting that IL-5 may also regulate B cellfunction, including IgE synthesis, by autocrine mechanisms.

The invention provides methods of evolving an IL-5 antagonist thatefficiently binds to and neutralizes IL-5 or its receptor. Theseantagonists are useful as a component of vaccines used for prophylaxisand treatment of allergies. Nucleic acids encoding IL-5, for example,from human and other mammalian species, are experimentally evolved (e.g.by polynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) and screened for binding to immobilized IL-5R for theinitial screening. Polypeptides that exhibit the desired effect in theinitial screening assays can then be screened for the highest biologicalactivity using assays such as inhibition of growth of IL-5 dependentcells lines cultured in the presence of recombinant wild-type IL-5.Alternatively, experimentally evolved (e.g. by polynucleotide reassembly&/or polynucleotide site-saturation mutagenesis) IL-5R α-chains arescreened for improved binding to IL-5.

Tumor necrosis factors (α and β) and their receptors are also suitabletargets for modification and use in genetic vaccines. TNF-α, which wasoriginally described as cachectin because of its ability to causenecrosis of tumors, is a 17 kDa protein that is produced in lowquantities by almost all cells in the human body following activation.TNF-α acts as an endogenous pyrogen and induces the synthesis of severalproinflammatory cytokines, stimulates the production of acute phaseproteins, and induces proliferation of fibroblasts. TNF-α plays a majorrole in the pathogenesis of endotoxin shock. A membrane-bound form ofTNF-α (mTNF-α), which is involved in interactions between B- andT-cells, is rapidly upregulated within four hours of T cell activation.mTNF-α plays a role in the polyclonal B cell activation observed inpatients infected with HIV. Monoclonal antibodies specific for mTNF-α orthe p55 TNF-α receptor strongly inhibit IgE synthesis induced byactivated CD4⁺ T cell clones or their membranes. Mice deficient for p55TNF-αR are resistant to endotoxic shock, and soluble TNF-αR preventsautoimmune diabetes mellitus in NOD mice. Phase III trials using sTNF-αRin the treatment of rheumatoid arthritis are in progress, afterpromising results obtained in the phase II trials.

The methods of the invention can be used to, for example, evolve asoluble TNF-αR that has improved affinity, and thus is capable of actingas an antagonist for TNF activity. Nucleic acids that encode TNF-αR andexhibit sequence diversity, such as the natural diversity observed incDNA libraries from activated T cells of human and other primates, areexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis). The experimentally evolved(e.g. by polynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) nucleic acids are expressed, e.g., on phage, after whichmutants are selected that bind to TNF-α with improved affinity. Ifdesired, the improved mutants can be subjected to further assays usingbiological activity, and the experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) genes can be subjected to one or more rounds of reassembly(optionally in combination with other directed evolution methodsdescribed herein) and screening.

Another target of interest for application of the methods of theinvention is interferon-K, and the evolution of antagonists of thiscytokine. The receptor for IFN-γ consists of a binding componentglycoprotein of 90 kD, a 228 amino acid extracellular portion, atransmembrane region, and a 222 amino acid intracellular region.Glycosylation is not required for functional activity. A single chainprovides high affinity binding (10⁻⁹-10⁻¹⁰ M), but is not sufficient forsignaling. Receptor components dimerize upon ligand binding.

The mouse IFN-γ receptor is 53% identical to that of mouse at the aminoacid level. The human and mouse receptors only bind human and mouseIFN-γ, respectively. Vaccinia, cowpox and camelpox viruses havehomologues of sIFN-γ R, which have relatively low amino acid sequencesimilarity (˜20%), but are capable of efficient neutralization of IFN-γin vitro. These homologues bind human, bovine, rat (but not mouse)IFN-γ, and may have in vivo activity as IFN-γ antagonists. All eightcysteines are conserved in human, mouse, myxoma and Shope fibroma virus(6 in vaccinia virus) IFN-γ R polypeptides, indicating similar 3-Dstructures. An extracellular portion of m IFN-γR with a kD of 100-300 μMhas been expressed in insect cells. Treatment of NZB/W mice (a mousemodel of human SLE) with msIFN-γ receptor (100 mg/three times a weeki.p.) inhibits the onset of glomerulonephritis. All mice treated withsIFN-γ or anti-IFN-γ niAbs were alive 4 weeks after the treatment wasdiscontinued, compared with 50% in a placebo group, and 78% ofIFN-γ-treated mice died.

The methods of the invention can be used to evolve soluble IFN-γRreceptor polypeptides with improved affinity, and to evolve IFN-γ withimproved specific activity and improved capacity to activate cellularimmune responses. In each case nucleic acids encoding the respectivepolypeptide, and which exhibit sequence diversity (e.g., that observedin cDNA libraries from activated T cells from human and other primates),are subjected to reassembly (&/or one or more additional directedevolution methods described herein) and screened to identify thoserecombinant nucleic acids that encode a polypeptide having improvedactivity. In the case of experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis) IFN-γR, thelibrary of experimentally evolved (e.g. by polynucleotide reassembly&/or polynucleotide site-saturation mutagenesis) nucleic acids can beexpressed on phage, which are screened to identify mutants that bind toIFN-γ with improved affinity. In the case of IFN-γ, the experimentallyevolved (e.g. by polynucleotide reassembly &/or polynucleotidesite-saturation mutagenesis) library is analyzed for improved specificactivity and improved activation of the immune system, for example, byusing activation of monocytes/macrophages as an assay. The evolved IFN-γmolecules can improve the efficacy of vaccinations (e.g. when used asadjuvants). Diseases that can be treated using high-affinity sIFN-γRpolypeptides obtained using the methods of the invention include, forexample, multiple sclerosis, systemic lupus erythematosus (SLE), organrejection after treatment, and graft versus host disease. Multiplesclerosis, for example, is characterized by increased expression ofIFN-γ in the brain of the patients, and increased production of IFN-γ bypatients' T cells in vitro. IFN-γ treatment has been shown tosignificantly exacerbate the disease (in contrast to EAE in mice).

Transforming growth factor (TGF)-β is another cytokine that can beoptimized for use in genetic vaccines using the methods of theinvention. TGF-β has growth regulatory activities on essentially allcell types, and it has also been shown to have complex modulatoryeffects on the cells of the immune system. TGF-β inhibits proliferationof both B and T cells, and it also suppresses development of anddifferentiation of cytotoxic T cells and NK cells, TGF-β has been shownto direct IgA switching in both murine and human B cells. It was alsoshown to induce germline a transcription in murine and human B cells,supporting the conclusion that TGF-β can specifically induce IgAswitching.

Due to its capacity to direct IgA switching, TGF-β is useful as acomponent of DNA vaccines which aim at inducing potent mucosal immunity,e.g. vaccines for diarrhea. Also, because of its potentanti-proliferative effects TGF-β is useful as a component oftherapeutical cancer vaccines. TGF-β with improved specific activityand/or with improved expression levels/kinetics will have increasedbeneficial effects compared to the wild-type TGF-β.

Cytokines that can be optimized using the methods of the invention alsoinclude granulocyte colony stimulating factor (G-CSF) andgranulocyte/macrophage colony stimulating factor (GM-CSF). Thesecytokines induce differentiation of bone marrow stem cell intogranulocytes/macrophages. Administration of G-CSF and GM-CSFsignificantly improve recovery from bone marrow (BM) transplantation andradiotherapy, reducing infections and time the patients have to spend inhospitals. GM-CSF enhances antibody production following DNAvaccination. G-CSF is a 175 amino acid protein, while GM-CSF has 127amino acids. Human G-CSF is 73% identical at the amino acid level tomurine G-CSF and the two proteins show species cross-reactivity. G-CSFhas a homodimeric receptor (dimeric with kD of ˜200 pM, monomeric ˜2.4nM), and the receptor for GM-CSF is a three subunit complex. Cell linestransfected with cDNA encoding G-CSF R proliferate in response to G-CSF.Cell lines dependent of GM-CSF available (such as TF-1). G-CSF isnontoxic and is presently working very well as a drug. However, thetreatment is expensive, and more potent G-CSF might reduce the cost forpatients and to the health care. Treatments with these cytokines aretypically short-lasting and the patients are likely to never need thesame treatment again reducing likelihood of problems withimmunogenicity.

The methods of the invention are useful for evolving G-CSF and/or GM-CSFwhich have improved specific activity, as well as other polypeptidesthat have G-CSF and/or GM-CSF activity. G-CSF and/or GM-CSF nucleicacids having sequence diversity, e.g., those obtained from cDNAlibraries from diverse species, are experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) to create a library of experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) G-CSF and/or GM-CSF genes. These libraries can be screenedby, for example, picking colonies, transfecting the plasmids into asuitable host cell (e.g., CHO cells), and assaying the supernatantsusing receptor-positive cell lines. Alternatively, phage display orrelated techniques can be used, again using receptor-positive celllines. Yet another screening method involves transfecting theexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) genes intoG-CSF/GM-CSF-dependent cell lines. The cells are grown one cell per welland/or at very low density in large flasks, and the cells that growfastest are selected. Experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis) genes fromthese cells are isolated; if desired, these genes can be used foradditional rounds of reassembly (optionally in combination with otherdirected evolution methods described herein) and selection.

Ciliary neurotrophic factor (CNTF) is another suitable target forapplication of the methods of the invention. CNTF has 200 amino acidswhich exhibit 80% sequence identity between rat and rabbit CNTFpolypeptides. CNTF has IL-6-like inflammatory effects, and inducessynthesis of acute phase proteins. CNTF is a cytosolic protein whichbelongs to the IL-6/IL-11/LIF/oncostatin M-family, and becomesbiologically active only after becoming available either by cellularlesion or by an unknown release mechanism. CNTF is expressed bymyelinating Schwann cells, astrocytes and sciatic nerves.

Structurally, CNTF is a dimeric protein, with a novel anti-parallelarrangement of the subunits. Each subunit adopts a double crossoverfour-helix bundle fold, in which two helices contribute to the dimerinterface. Lys-155 mutants lose activity, and some Glu-153 mutants have5-10 higher biological activity. The receptor for CNTF consists of aspecific CNTF receptor chain, gp130, and a LIF-β receptor. The CNTFRα-chain lacks a transmembrane domain portion, instead beingGPI-anchored. At high concentration, CNTF can mediate CNTFR-independentresponses. Soluble CNTFR binds CNTF and thereafter can bind to LIFR andinduce signaling through gp 130. CNTF enhances survival of several typesof neurons, and protects neurons in an animal model of Huntingtondisease (in contrast to NGF, neurotrophic factor, and neurotrophin-3).CNTF receptor knockout mice have severe motor neuron deficits at birth,and CNTF knockout mice exhibit such deficits postnatally. CNTF alsoreduces obesity in mouse models. Decreased expression of CNTF issometimes observed in psychiatric patients. Phase I studies in patientswith ALS (annual incidence ˜1/100 000, 5% familiar cases, 90% die within6 years) found significant side effects after doses higher than 5mg/kg/day subcutaneously (including anorexia, weight loss, reactivationof herpes simplex virus (HSV1), cough, increased oral secretions).Antibodies against CNTF were detected in almost all patients, thusillustrating the need for alternative CNTF with different immunologicalproperties.

The reassembly (&/or one or more additional directed evolution methodsdescribed herein) and screening methods of the invention can be used toobtain modified CNTF polypeptides that exhibit decreased immunogenicityin vivo; higher also obtainable using the methods. Reassembly(optionally in combination with other directed evolution methodsdescribed herein) is conducted using nucleic acids encoding CNTF. In apreferred embodiment, an IL-6/LIF/(CNTF) hybrid is obtained byreassembly (optionally in combination with other directed evolutionmethods described herein) using an excess of oligonucleotides thatencode to the receptor binding sites of CNTF. Phage display can then beused to test for lack of binding to the IL-6/LIF receptor.

This initial screen is followed by a test for high affinity binding tothe CNTF receptor, and, if desired, functional assays using CNTFresponsive cell lines. The experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) CNTF polypeptides can be tested to identify those thatexhibit reduced immunogenicity upon administration to a mammal.

Another way in which the reassembly (&/or one or more additionaldirected evolution methods described herein) and screening methods ofthe invention can be used to optimize CNTF is to improve secretion ofthe polypeptide. When a CNTF cDNA is operably linked to a leadersequence of hNGF, only 3540 percent of the total CNTF produced issecreted.

Target diseases for treatment with optimized CNTF, using either theexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) gene in an expression vectoras in DNA vaccines, or a purified protein, include obesity, amyotrophiclateral sclerosis (ALS, Lou Gehrig's disease), diabetic neuropathy,stroke, and brain surgery.

Polynucleotides that encode chemokines can also be optimized using themethods of the invention and included in a genetic vaccine vector. Atleast three classes of chemokines are known, based on structure: Cchemokines (such as lymphotactin), C—C chemokines (such as MCP-1, MCP-2,MCP-3, MCP-4, MIP-1α, MIP-1b, RANTES), C—X—C chemokines (such as IL-8,SDF-1, ELR, Mig, IP 10) (Premack and Schall (1996) Nature Med. 2: 1174).Chemokines can attract other cells that mediate immune and inflammatoryfunctions, thereby potentiating the immune response. Cells that areattracted by different types of chemokines include, for example,lymphocytes, monocytes and neutrophils. Generally, C—X—C chemokines arechemoattractants for neutrophils but not for monocytes, C—C chemokinesattract monocytes and lymphocytes but not neutrophils, C chemokineattracts lymphocytes.

Genetic vaccine vectors can also include optimized experimentallygenerated polynucleotides that encode surface-bound accessory molecules,such as those that are involved in modulation and potentiation of immuneresponses. These molecules, which include, for example, B7-1 (CD80),B7-2 (CD86), CD40, ligand for CD40, CTLA-4, CD28, and CD 150 (SLAM), canbe subjected to stochastic (e.g. polynucleotide shuffling & interruptedsynthesis) and non-stochastic polynucleotide reassembly to obtainvariants have altered and/or improved activities.

Optimized experimentally generated polynucleotides that encode CD1molecules are also useful in a genetic vaccine vector for certainapplications. CD1 are nonpolymorphic molecules that are structurally andfunctionally related to MEC molecules. Importantly, CD1 has MHC-likeactivities, and it can function as an antigen presenting molecule(Porcelli (1995) Adv. Immunol. 59: 1). CD1 is highly expressed ondendritic cells, which are very efficient antigen presenting cells.Simultaneous transfection of target cells with DNA vaccine vectorsencoding CD1 and an antigen of interest is likely to boost the immuneresponse. Because CD1 cells, in contrast to MHC molecules, exhibitlimited allelic diversity in an outbred population (Porcelli, supra.),large populations of individuals with different genetic backgrounds canbe vaccinated with one CD1 allele. The functional properties of CD1molecules can be improved by the stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly methods of the invention.

Optimized recombinant TAP genes and/or gene products can also beincluded in a genetic vaccine vector. TAP genes and their optimizationfor various purposes are discussed in more detail below. Moreover, heatshock proteins (HSP), such as HSP70, can also be evolved for improvedpresentation and processing of antigens. HSP70 has been shown to act asadjuvant for induction of CD8⁺ T cell activation and it enhancesimmunogenicity of specific antigenic peptides (Blachere et al. (1997) JExp. Med. 186:1315-22). When HSP70 is encoded by a genetic vaccinevector, it is likely to enhance presentation and processing of antigenicpeptides and thereby improve the efficacy of the genetic vaccines.Stochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly can be used to further improvethe properties, including adjuvant activity, of heat shock proteins,such as HSP70.

Recombinantly produced cytokine, chemokine, and accessory moleculepolypeptides, as well as antagonists of these molecules, can be used toinfluence the type of immune response to a given stimulus. However, theadministration of polypeptides sometimes has shortcomings, includingshort half life, high expense, difficult to store (must be stored at 4°C.), and a requirement for large volumes. Also, bolus injections cansometimes cause side effects. Administration of polynucleotides thatencode the recombinant cytokines or other molecules overcomes most orall of these problems. DNA, for example, can be prepared in high purity,is stable, temperature resistant, noninfectious, easy to manufacture. Inaddition, polynucleotide-mediated administration of cytokines canprovide long-lasting, consistent expression, and administration ofpolynucleotides in general is regarded as being safe.

The functions of cytokines, chemokines and accessory molecules areredundant and pleiotropic, and therefore can be difficult to determinewhich cytokines or cytokine combinations are the most potent in inducingand enhancing antigen specific immune responses following vaccination.Furthermore, the most useful combination of cytokines and accessorymolecules is typically different depending on the type of immuneresponse that is desired following vaccination. As an example, IL-4 hasbeen shown to direct differentiation of T_(H)2 cells (which produce highlevels of IL-4, IL-5 and IL-13, and mediate allergic immune responses),whereas IFN-γ and IL-12 direct differentiation of T_(H)1 cells (whichproduce high levels of IL-2 and IFN-γ), and mediate delayed type immuneresponses. Moreover, the most useful combination of cytokines andaccessory molecules is also likely to depend on the antigen used in thevaccination. The invention provides a solution to this problem ofobtaining an optimized genetic vaccine cocktail. Different combinationsof cytokines, chemokines and accessory molecules are assembled intovectors using the methods described herein. These vectors are thenscreened for their capacity to induce immune responses in vivo and invitro.

Large libraries of vectors, generated by polynucleotide (e.g. gene,promoter, enhancer, intron, & the like) reassembly (optionally incombination with other directed evolution methods described herein) andcombinatorial molecular biology, are screened for maximal capacity todirect immune responses towards, for example, a T_(H)1 or T_(H)2phenotype, as desired. A library of different vectors can be generatedby assembling different evolved promoters, (evolved) cytokines,(evolved) cytokine antagonists, (evolved) chemokines, (evolved)accessory molecules and immunostimulatory sequences, each of which canbe prepared using methods described herein. DNA sequences and compoundsthat facilitate the transfection and expression can be included. If thepathogen(s) is known, specific DNA sequences encoding immunogenicantigens from the pathogen can be incorporated into these vectorsproviding protective immunity against the pathogen(s) (as in geneticvaccines).

Initial screening is preferably carried out in vitro. For example, thelibrary can be introduced into cells which are tested for ability toinduce differentiation of T cells capable of producing cytokines thatare indicative of the type of immune response desired. For a T_(H)1response, for example, the library is screened to identifyexperimentally generated polynucleotides that are capable of inducing Tcells to produce IL-2 and IFN-γ, while screening for induction of T cellproduction of IL-4, IL-5, and IL-13 is performed to identifyexperimentally generated polynucleotides that favor a T_(H)2 response.

Screening can also be conducted in vivo, using animal models. Forexample, vectors produced using the methods of the invention can betested for ability to protect against a lethal infection. Anotherscreening method involves injection of Leishmania major parasites intofootpads of BALB/c mice (nonhealer). Pools of plasmids are injectedi.v., i.p. or into footpads of these mice and the size of the footpadswelling is followed. Yet another in vivo screening method involvesdetection of IgE levels after infection with Nippostrongylusbrasiliensis. High levels indicate a T_(H)2 response, while low levelsof IgE indicate a T_(H)1 response.

Successful results in animal models are easy to verify in humans. Invitro screening can be conducted to test for human T_(H)1 or T_(H)2phenotype, or for other desired immune response. Vectors can also betested for ability to induce protection against infection in humans.Because the principles of immune functions are similar in a wide varietyof infections, immunostimulating DNA vaccine vectors may not only beuseful in the treatment of a number of infectious diseases but also inprevention of the infections, when the vectors are delivered to thesites of the entry of the pathogen (e.g., the lung or gut).

2.6.5.3. Agonists or Antagonists of Cellular Receptors

The invention also provides methods for obtaining optimizedexperimentally generated polynucleotides that encode a peptide orpolypeptide that can interact with a cellular receptor that is involvedin mediating an immune response. The optimized experimentally generatedpolynucleotides can act as an agonist or an antagonist of the receptor.

Cytokine Antagonists can be Used as Components of Genetic VaccineCocktails

Blocking immunosuppressive cytokines, rather than adding singleproinflammatory cytokines, is likely to potentiate the immune responsein a more general manner, because several pathways are potentiated atthe same time. By appropriate choice of antagonist, one can tailor theimmune response induced by a genetic vaccine in order to obtain theresponse that is most effective in achieving the desired effect.Antagonists against any cytokine can be used as appropriate; particularcytokines of interest for blocking include, for example, IL-4, IL-13,IL-10, and the like.

The invention provides methods of obtaining cytokine antagonists thatexhibit greater effectiveness in blocking the action of the respectivecytokine. Polynucleotides that encode improved cytokine antagonists canbe obtained by using polynucleotide (e.g. gene, promoter, enhancer,intron, & the like) reassembly (optionally in combination with otherdirected evolution methods described herein) to generate a recombinantlibrary of polynucleotides which are then screened to identify thosethat encode an improved antagonist. As substrates for the stochastic(e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly, one can use, for example,polynucleotides that encode receptors for the respective cytokine. Atleast two forms of the substrate will be present in the reassembly (&/orone or more additional directed evolution methods described herein)reaction, with each form differing from the other in at least onenucleotide position. In a preferred embodiment, the different forms ofthe polynucleotide are homologous cytokine receptor genes from differentorganisms. The resulting library of experimentally generatedpolynucleotides is then screened to identify those that encode cytokineantagonists with the desired affinity and biological activity.

As one example of the type of effect that one can achieve by including acytokine antagonist in a genetic vaccine cocktail, as well as how theeffect can be improved using the stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly methods of the invention, IL-10 is discussed. The samerationale can be applied to obtaining and using antagonists of othercytokines. Interleukin-10 (IL-10) is perhaps the most potentanti-inflammatory cytokine known to date. IL-10 inhibits a number ofpathways that potentiate inflammatory responses. The biologicalactivities of IL-10 include inhibition of MHC class II expression onmonocytes, inhibition of production of IL-1, IL-6, IL-12, TNF-α bymonocytes/macrophages, and inhibition of proliferation and IL-2production by T lymphocytes. The significance of IL-10 as a regulatorymolecule of immune and inflammatory responses was clearly demonstratedin IL-10 deficient mice.

These mice are growth-retarded, anemic and spontaneously develop aninflammatory bowel disease (Kuhn et al. (1993) Cell 75: 263). Inaddition, both innate and acquired immunity to Listeria monocytogeneswere shown to be elevated in IL-10 deficient mice (Dai et al. (1997) JImmunol. 158: 2259). It has also been suggested that genetic differencesin the levels of IL-10 production may affect the risk of patients to diefrom complications meningococcal infection. Families with high IL-10production had 20-fold increased risk of fatal outcome of meningococcaldisease (Westendorp et al. (1997) Lancet 349: 170).

IL-10 has been shown to activate normal and malignant B cells in vitro,but it does not appear to be a major growth promoting cytokine fornormal B cells in vivo, because IL-10 deficient mice have normal levelsof B lymphocytes and Ig in their circulation. In fact, there is evidencethat IL-10 can indirectly downregulate B cell function throughinhibition of the accessory cell function of monocytes. However, IL-10appears to play a role in the growth and expansion of malignant B cells.Anti-IL-10 monoclonal antibodies and IL-10 antisense oligonucleotideshave been shown to inhibit transformation of B cells by EBV in vitro. Inaddition, B cell lymphomas are associated with EBV and most EBV⁺lymphomas produce high levels of IL-10, which is derived both from thehuman gene and the homologue of IL-10 encoded by EBV. AIDS-related Bcell lymphomas also secrete high levels of IL-10. Furthermore, patientswith detectable serum IL-10 at the time of diagnosis ofintermediate/high-grade non-Hodgkin's lymphoma have short survival,further suggesting a role for IL-10 in the pathogenesis of B cellmalignancies.

Antagonizing IL-10 in vivo can be beneficial in several infectious andmalignant diseases, and in vaccination. The effect of blocking of IL-10is an enhancement of immune responses that is independent of thespecificity of the response. This is useful in vaccinations and in thetreatment of serious infectious diseases. Moreover, an IL-10 antagonistis useful in the treatment of B cell malignancies which exhibitoverproduction of IL-10 and viral IL-10, and it may also be useful inboosting general anti-tumor immune response in cancer patients.Combining an IL-10 antagonist with gene therapy vectors may be useful ingene therapy of tumor cells in order to obtain maximal immune responseagainst the tumor cells. If the reassembly (optionally in combinationwith other directed evolution methods described herein) of IL-10 resultsin IL-10 with improved specific activity, this IL-10 molecule would havepotential in the treatment of autoimmune diseases and inflammatory boweldiseases. IL-10 with improved specific activity may also be useful as acomponent of gene therapy vectors in reducing the immune responseagainst vectors which are recognized by memory cells and it may alsoreduce the immunogenicity of these vectors.

An antagonist of IL-10 has been made by generating a soluble form ofIL-10 receptor (sIL-10R; Tan et al. (1995) J Biol. Chem. 270: 12906).However, sIL-10R binds IL-10 with Kd of 560 pM, whereas the wild-type,surface-bound receptor has affinity of 35-200 pM. Consequently, 150-foldmolar excess of sIL-10R is required for half-maximal inhibition ofbiological function of IL-10. Moreover, affinity of viral IL-10 (IL-10homologue encoded by Epstein-Barr virus) to sIL-10R is more than 1000fold less than that of hIL-10, and in some situations, such as whentreating EBV-associated B cell malignancies, it may be beneficial if onecan also block the function of viral IL-10. Taken together, this solubleform of IL-10R is unlikely to be effective in antagonizing IL-10 invivo.

To obtain an IL-10 antagonist that has sufficient affinity andantagonistic activity to function in vivo, stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly can be performed using polynucleotides thatencode IL-10 receptor. IL-10 receptor with higher than normal affinitywill function as an IL-10 antagonist, because it strongly reduces theamount of IL-10 available for binding to functional, wild-type IL-10R.In a preferred embodiment, IL-10R is experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) using homologous cDNAs encoding IL-10R derived from humanand other mammalian species.

An alignment of human and mouse IL-10 receptor sequences is shown,described &/or referenced herein (including incorporated by reference)to illustrate the feasibility of family stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly when evolving IL-10 receptors with improved affinity. A phagelibrary of IL-10 receptor recombinants can be screened for improvedbinding of experimentally evolved (e.g. by polynucleotide reassembly&/or polynucleotide site-saturation mutagenesis) IL-10R to human orviral IL-10. Wild-type IL-10 and/or viral IL-10 are added at increasingconcentrations to demand for higher affinity. Phage bound to IL-10 canbe recovered using anti-IL-10 monoclonal antibodies. If desired, theshuffling can be repeated one or more times, after which the evolvedsoluble IL-1 OR is analyzed in functional assays for its capacity toneutralize the biological activities of IL-10/viral IL-10. Morespecifically, evolved soluble IL-10R is studied for its capacity toblock the inhibitory effects of IL-10 on cytokine synthesis and MHCclass II expression by monocytes, proliferation by T cells, and for itscapacity to inhibit the enhancing effects of IL-10 on proliferation of Bcells activated by anti-CD40 monoclonal antibodies.

An IL-10 antagonist can also be generated by evolving IL-10 to obtainvariants that bind to IL-10R with higher than wild-type affinity, butwithout receptor activation. The advantage of this approach is that onecan evolve an IL-10 molecule with improved specific activity using thesame methods. In a preferred embodiment, IL-10 is experimentally evolved(e.g. by polynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) using homologous cDNAs encoding IL-10 derived from humanand other mammalian species. In addition, a gene encoding viral IL-10can be included in the reassembly (optionally in combination with otherdirected evolution methods described herein). A library of IL-10recombinants is screened for improved binding to human IL-10 receptor.Library members bound to IL-10R can be recovered by anti-IL-10Rmonoclonal antibodies. This screening protocol is likely to result inIL-10 molecules with both antagonistic and agonistic activities. Becauseinitial screen demands for higher affinity, a proportion of the agonistsare likely to have improved specific activity when compared to wild-typehuman IL-10. The functional properties of the mutant IL-10 molecules aredetermined in biological assays similar to those described above forultrahigh-affinity IL-10 receptors (cytokine synthesis and MHC class IIexpression by monocytes, proliferation of B and T cells). Anantagonistic IL-4 mutant has been previously generated illustrating thegeneral feasibility of the approach (Kruse et al. (1992) EMBO J. 11:3237-3244). One amino acid mutation in IL-4 resulted in a molecule thatefficiently binds to IL-4R α-chain but has minimal IL-4-like agonisticactivity.

Another example of an IL-10 antagonist is IL-20/mda-7, which is a 206amino acid secreted protein. This protein was originally characterizedas mda-7, which is a melanoma cell-derived negative regulator of tumorcell growth (Jiang et al. (1995) Oncogene 11: 2477; (1996) Proc. Nat'l.Acad. Sci. USA 93: 9160). IL-20/mda-7 is structurally related to IL-10,and it antagonizes several functions of IL-10 (Abstract of the 13^(th)European Immunology Meeting, Amsterdam, 22-25 Jun. 1997). In contrast toIL-10, IL-20/mda-7 enhances expression of CD80 (B7-1) and CD86 (B7-2) onhuman monocytes and it upregulates production of TNF-α and IL-6.IL-20/mda-7 also enhances production of IFN-γ by PHA-activated PBMC. Theinvention provides methods of improving genetic vaccines byincorporation of IL-20/mda-7 genes into the genetic vaccine vectors. Themethods of the invention can be used to obtain IL-20/mda-7 variants thatexhibit improved ability to antagonize IL-10 activity.

When a cytokine antagonist is used as a component of DNA vaccine or genetherapy vectors, maximal local effect is desirable. Therefore, inaddition to a soluble form of a cytokine antagonist, a transmembraneform of the antagonist can be generated. The soluble form can be givenin purified polypeptide form to patients by, for example, intravenousinjection. Alternatively, a polynucleotide encoding the cytokineantagonist can be used as a component as a component of a geneticvaccine or a gene therapy vector. In this case, either or both of thesoluble and transmembrane forms can be used. Where both soluble andtransmembrane forms of the antagonist are encoded by the same vector,the target cells express both forms, resulting in maximal inhibition ofcytokine function on the target cell surface and in their immediatevicinity.

The peptides or polypeptides obtained using these methods can substitutefor the natural ligands of the receptors, such as cytokines or othercostimulatory molecules in their ability to exert an effect on theimmune system via the receptor. A potential disadvantage ofadministering cytokines or other costimulatory molecules themselves isthat an autoimmune reaction could be induced against the naturalmolecule, either due to breaking tolerance (if using a natural cytokineor other molecule) or by inducing cross-reactive immunity (humoral orcellular) when using related but distinct molecules. Through using themethods of the invention, one can obtain agonists or antagonists thatavoid these potential drawbacks. For example, one can use relativelysmall peptides as agonists that can mimic the activity of the naturalimmunomodulator, or antagonize the activity, without inducingcross-reactive immunity to the natural molecule. In a presentlypreferred embodiment, the optimized agonist or antagonist obtained usingthe methods of the invention is about 50 amino acids in length or less,more preferably about 30 amino acids or less, and most preferably isabout 20 amino acids in length, or less. The agonist or antagonistpeptide is preferably at least about 4 amino acids in length, and morepreferably at least about 8 amino acids in length. Polynucleotides thatflank the coding sequence of the mimetic peptide can also be optimizedusing the methods of the invention in order to optimize the expression,conformation, or activity of the mimetic peptide.

The optimized agonist or antagonist peptides or polypeptides areobtained by generating a library of experimentally generatedpolynucleotides and screening the library to identify those that encodea peptide or polypeptide that exhibits an enhanced ability to modulatean immune response. The library can be produced using methods such asstochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly or other methods describedherein or otherwise known to those of skill in the art. Screening isconveniently conducted by expressing the peptides encoded by the librarymembers on the surface of a population of replicable genetic packagesand identifying those members that bind to a target of interest, e.g., areceptor.

The optimized experimentally generated polynucleotides that are obtainedusing the methods of the invention can be used in several ways. Forexample, the polynucleotide can be placed in a genetic vaccine vector,under the control of appropriate expression control sequences, so thatthe mimetic peptide is expressed upon introduction of the vector into amammal. If desired, the polynucleotide can be placed in the vectorembedded in the coding sequence of the surface protein (e.g., geneIII orgeneVIII) in order to preserve, the conformation of the mimetic.Alternatively, the mimetic-encoding polynucleotide can be inserteddirectly into the antigen-encoding sequence of the genetic vaccine toform a coding sequence for a “mimotope-on-antigen” structure. Thepolynucleotide that encodes the mimotope-on-antigen structure can beused within a genetic vaccine, or can be used to express a protein thatis itself administered as a vaccine. As one example of this type ofapplication, a coding sequence of a mimetic peptide is introduced into apolynucleotide that encodes the “M-loop” of the hepatitis B surfaceantigen (HBsAg) protein. The M-loop is a six amino acid peptide sequencebounded by cysteine residues, which is found at amino acids 139-147(numbering within the S protein sequence). The M-loop in the naturalHBsAg protein is recognized by the monoclonal antibody RFHB7 (Chen etal., Proc. Nat'l. Acad. Sci. USA, 93: 1997-2001 (1996)). According toChen et al., the M-loop forms an epitope of the HBsAg that isnon-overlapping and separate from at least four other HBsAg epitopes.

Because of the probable Cys-Cys disulfide bond in this hydrophilic partof the protein, amino acids 139-147 are likely in a cyclic conformation.This structure is therefore similar to that found in the regions of thefilamentous phage proteins pIII and pVIII where mimotope sequences areplaced. Therefore, one can insert a mimotope obtained using the methodsof the invention into this region of the HBsAg amino acid sequence.

The chemokine receptor CCR6 is an example of a suitable target for apeptide mimetic obtained using the methods. The CCR6 receptor is a7-transmembrane domain protein (Dieu et al., Biochem. Biophys. Res.Comm. 236: 212-217 (1997) and J. Biol. Chem. 272: 14893-14898 (1997))that is involved in the chemoattraction of immature dendritic cells,which are found in the blood and migrate to sites of antigen uptake(Dieu et al., J Exp. Med. 188: 373-386 (1998)). CCR6 binds the chemokineMIP-3α, so a mimetic peptide that is capable of activating CCR6 canprovide a further chemoattractant function to a given antigen and thuspromote uptake by dendritic cells after immunization with the antigenantigen-mimetic fusion or a DNA vector that expresses the antigen.

Another application of this method of the invention is to obtainmolecules that can act as an agonist for the macrophage scavengerreceptor (MSR; see, Wloch et al., Hum. Gene Ther. 9: 1439-1447 (1998)).The MSR is involved in mediating the effects of variousimmunomodulators. Among these are bacterial DNA, including the plasmidsused in DNA vaccination, and oligonucleotides, which are often potentimmunostimulators.

Oligonucleotides of certain chemical structure (e.g.,phosphothio-oligonucleotides) are particularly potent, while bacterialor plasmid DNA must be used in relatively large quantities to produce aneffect. Also mediated by the MSR is the ability of oligonucleotides thatcontain dG residues to stimulate B cells and enhance the activity ofimmunostimulatory CpG motifs, and of lipopolysaccharides to activatemacrophages. Some of these activities are toxic. Each of theseimmunomodulators, along with a variety of polyanionic ligands, binds tothe MSR. The methods of the invention can be used to obtain mimetics ofone or more of these immunomodulators that bind to the MSR with highaffinity but are devoid of toxic properties. Such mimetic peptides areuseful as immunostimulators or adjuvants.

The MSR is a trimeric integral membrane glycoprotein. The threeextracellular C-terminal cysteine-rich regions are connected to thetransmembrane domain by a fibrous region that is composed of an(α-helical coil and a collagen-like triple helix (see, Kodama et al.,Nature 343: 531-535 (1990)). Therefore, screening of the library ofexperimentally generated polynucleotides can be accomplished byexpressing the extracellular receptor structure and artificiallyattaching it to plastic surfaces. The libraries can be expressed, e.g.,by phage display, and screened to identify those that bind to thereceptors with high affinity.

The optimized experimentally generated polynucleotides identified bythis method can be incorporated into antigen-encoding sequences toevaluate their modulatory effect on the immune response.

2.6.5.4. Costimulatory Molecules Capable of Inhibiting or EnhancingActivation, Differentiation, or Anergy of Antigen-Specific T Cells

Also provided are methods of obtaining optimized experimentallygenerated polynucleotides that, when expressed, are capable ofinhibiting or enhancing the activation, differentiation, or anergy ofantigen-specific T cells. T cell activation is initiated when T cellsrecognize their specific antigenic peptides in the context of MHCmolecules on the plasma membrane of antigen presenting cells (APC), suchas monocytes, dendritic cells (DC), Langerhans cells or B cells.Activation of CD4⁺ T cells requires recognition by the T cell receptor(TCR) of an antigenic peptide in the context of MHC class II molecules,whereas CD8⁺ T cells recognize peptides in the context of MHC class Imolecules.

Importantly, however, recognition of the antigenic peptides is notsufficient for induction of T cell proliferation and cytokine synthesis.An additional costimulatory signal, “the second signal”, is required.The costimulatory signal is mediated via CD28, which binds to itsligands B7-1 (CD80) or B7-2 (CD86), typically expressed on the antigenpresenting cells. In the absence of the costimulatory signal, no T cellactivation occurs, or T cells are rendered anergic. In addition to CD28,CTLA-4 (CD152) also functions as a ligand for B7-1 and B7-2. However, incontrast to CD28, CTLA-4 mediates a negative regulatory signal to Tcells and/or to induce anergy and tolerance (Walunas et al. (1994)Immunity 1: 405; Karandikar et al. (1996) J Exp. Med. 184: 783).

B7-1 and B7-2 have been shown to be able to regulate severalimmunological responses, and they have been implicated to be ofimportance in the immune regulation in vaccinations, allergy,autoimmunity and cancer. Gene therapy and genetic vaccine vectorsexpressing B7-1 and/or B7-2 have also been shown to have therapeuticpotential in the treatment of the above mentioned diseases and inimproving the efficacy of genetic vaccines.

FIG. 39 illustrates interaction of APC and CD4⁺ T cells, but the sameprinciple is true with CD8⁺ T cells, with the exception that the T cellsrecognize the antigenic peptides in the context of MHC class 1molecules. Both B7-1 and B7-2 bind to CD28 and CTLA-4, even though thesequence similarities between these four molecules are very limited(20-30%). It is desirable to obtain mutations in B7-1 and B7-2 that onlyinfluence binding to one ligand but not to the other, or improveactivity through one ligand while decreasing the activity through theother. Moreover, because the affinities of B7 molecules to their ligandsappear to be relatively low, it would also be desirable to findmutations that improve/alter the activities of the molecules. However,rational design does not enable predictions of useful mutations becauseof the complexity of the molecules.

The invention provides methods of overcoming these difficulties,enabling one to generate and identify functionally different B7molecules with altered relative capacities to induce T cell activation,differentiation, cytokine production, anergy and/or tolerance. Throughuse of the methods of the invention, one can find mutations in B7-1 andB7-2 that only influence binding to one ligand but not to the other, orthat improve activity through one ligand while decreasing the activitythrough the other by stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassembly islikely to be the most powerful method in discovering new B7 variantswith altered relative binding capacities to CD28 and CTLA-4. B7 variantswhich act through CD28 with improved activity (and with decreasedactivity through CTLA-4) are expected to have improved capacity toinduce activation of T cells. In contrast, B7 variants which bind andact through CTLA-4 with improved activity (and with decreased activitythrough CD28) are expected to be potent negative regulators of T cellfunctions and to induce tolerance and anergy.

Stochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly or other reassembly (&/or oneor more additional directed evolution methods described herein) methodis used to generate B7 (e.g., B7-1/CD80 and B7-2/CD86) variants whichhave altered relative capacity to act through CD28 and CTLA-4 whencompared to wild-type B7 molecules. In a preferred embodiment, thedifferent forms of substrate used in the reassembly (&/or one or moreadditional directed evolution methods described herein) reaction are B7cDNAs from various species. Such cDNAs can be obtained by methods knownto those of skill in the art, including RT-PCR. Typically, genesencoding these variant B7 molecules are incorporated into geneticvaccine vectors encoding an antigen, so that one the vectors can be usedto modify antigen-specific T cell responses. Vectors that harbor B7genes that efficiently act through CD28 are useful in inducing, forexample, protective immune responses, whereas vectors that harbor genesencoding B7 genes that efficiently act through CTLA-4 are useful ininducing, for example, tolerance and anergy of allergen- orautoantigen-specific T cells. In some situations, such as in tumor cellsor cells inducing autoimmune reactions, the antigen may already bepresent on the surface of the target cell, and the variant B7 moleculesmay be transfected in the absence of additional exogenous antigen gene.A screening protocol that one can use to identify B7-1 (CD80) and/orB7-2 (CD86) variants that have increased capacity to induce T cellactivation or anergy is diagrammed herein, and the application of thisstrategy is described in more detail herein.

Several approaches for screening of the variants can be taken. Forexample, one can use a flow cytometry-based selection systems. Thelibrary of B7-1 and B7-2 molecules is transfected into cells thatnormally do not express these molecules (e.g., COS-7 cells or any cellline from a different species with limited or no cross-reactivity withman regarding B7 ligand binding). An internal marker gene can beincorporated in order to analyze the copy number per cell. SolubleCTLA-4 and CD28 molecules can be generated to for use in the flowcytometry experiments. Typically, these will be fused with the Fcportion of IgG molecule to improve the stability of the molecules and toenable easy staining by labeled anti-IgG mAbs, as described by van derMerwe et al. (J. Exp. Med: 185: 393, 1997). The cells transfected withthe library of B7 molecules are then stained with the soluble CTLA-4 andCD28 molecules. Cells demonstrating increased or decreased CTLA-4/CD28binding ratio will be sorted. The plasmids are then recovered and theexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) B7 variant-encodingsequences identified. These selected B7 variants can then be subjectedto new rounds of reassembly (optionally in combination with otherdirected evolution methods described herein) and selection, and/or theycan be further analyzed using functional assays as described below.

The B7 variants can also be directly selected based on their functionalproperties. For in vivo studies, the B7 molecules can also be evolved tofunction on mouse cells. Bacterial colonies with plasmids with mutant B7molecules are picked and the plasmids are isolated. These plasmids arethen transfected into antigen presenting cells, such as dendritic cells,and the capacities of these mutants to activate T cells is analyzed. Oneof the advantages of this approach is that no assumptions on the bindingaffinities or specificities to the known ligands are made, and possiblynew activities through yet to be identified ligands can be found. Inaddition to dendritic cells, other cells that are relatively easy totransfect (e.g., U937 or COS-7) can be used in the screening, providedthat the “first T cell signal” is induced by, for example, anti-CD3monoclonal antibodies. T cell activation can be analyzed by methodsknown to those of skill in the art, including, for example, measuringproliferation, cytokine production, CTL activity or expression ofactivation antigens such as IL-2 receptor, CD69 or HLA-DR molecules.Usage of antigen-specific T, cell clones, such as T cells specific forhouse dust mite antigen Der p I, will allow analysis of antigen-specificT cell activation (Yssel et al. (1992) J Immunol. 148: 738-745). Mutantsare identified that can enhance or inhibit T cell proliferation orenhance or inhibit CTL responses. Similarly variants that have alteredcapacity to induce cytokine production or expression of activationantigens as measured by, for example, cytokine-specific ELISAs or flowcytometry can be identified.

The B7 variants are useful in modulating immune responses in autoimmunediseases, allergy, cancer, infectious disease and vaccination. B7variants which act through CD28 with improved activity (and withdecreased activity through CTLA-4) will have improved capacity to induceactivation of T cells. In contrast, B7 variants which bind and actthrough CTLA-4 with improved activity (and with decreased activitythrough CD28) will be potent negative regulators of T cell functions andto induce tolerance and anergy. Thus, by incorporating genes encodingthese variant B7 molecules into genetic vaccine vectors encoding anantigen, it is possible to modify antigen-specific T cell responses.Vectors that harbor B7 genes that efficiently act through CD28 areuseful in inducing, for example, protective immune responses, whereasvectors that harbor genes encoding B7 genes that efficiently act throughCTLA-4 are useful in inducing, for example, tolerance and anergy ofallergen- or autoantigen-specific T cells. In some situations, such asin tumor cells or cells inducing autoimmune reactions, the antigen mayalready be present on the surface of the target cell, and the variant B7molecules may be transfected in the absence of additional exogenousantigen gene.

The methods of the invention are also useful for obtaining B7 variantsthat have increased effectiveness in directing either T_(H)1 or T_(H)2cell differentiation. Differential roles have been observed for B7-1 andB7-2 molecules in the regulation of T helper (T_(H)) celldifferentiation (Freeman et al. (1995) Immunity 2: 523; Kuchroo et al.(1995) Cell 80: 707). T_(H) cell differentiation can be measured byanalyzing, the cytokine production profiles induced by each particularvariant. High levels of IL-4, IL-5 and/or IL-13 are an indication ofefficient T_(H)2 cell differentiation whereas high levels of IFN-γ orIL-2 production can be used as a marker of T_(H)1 cell differentiation.B7 variants with altered capacity to induce T_(H)1 or T_(H)2 celldifferentiation are useful, for example, in the treatment of allergic,malignant, autoimmune and infectious diseases and in vaccination.

Also provided by the invention are methods of obtaining B7 variants thathave enhanced capacity to induce IL-10 production by antigen-specific Tcells. Elevated production of IL-10 is a characteristic of regulatory Tcells, which can suppress proliferation of antigen-specific CD4⁺ T cells(Groux et al. (1997) Nature 389: 737). Stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly is performed as described above, after which recombinantnucleic acids encoding B7 variants having enhanced capability ofinducing IL-10 can be identified by, for example, ELISA or flowcytometry using intracytoplasmic cytokine staining. The variants thatinduce high levels of IL-10 production are useful in the treatment ofallergic and autoimmune diseases.

2.6.6. Evolution of Genetic Vaccine Vectors for Increased VaccinationEfficacy and Ease of Vaccination

This section discusses the application of the invention to some specificgoals in genetic vaccination. Many of these goals relate to improvementsin vectors used in vaccine delivery. Unless otherwise indicated themethods are applicable to both viral and nonviral vectors.

0.0.0.0. Topical Application of Genetic Vaccine Vectors

Low Efficiency of Topical Application; Protective Immune Responses havenot been Demonstrated

The invention provides methods of improving the ability of geneticvaccine vectors to induce a desired response after topical applicationof the vector. Adenoviral vectors topically applied to bare skin havebeen shown to be capable of acting as vaccine antigen delivery vehicles(Tang et al. (1997) Nature 388: 729-730). An adenoviral vector thatencoded carcinoembryonic antigen (CA) was shown to induce antibodiesspecific for CA after application to the skin. However, the efficiencyof topical application is generally quite low, and protective immuneresponses have not been demonstrated after topical application.

Optimizing the Topical Application Efficiency Using the Methods of theInvention

The invention provides methods of obtaining vectors that exhibitimproved efficiency when topically administered. Several factors caninfluence topical application efficiency, each of which can be optimizedusing the methods of the invention. For example, the invention providesmethods of improving vector affinity for skin cells, improved skin celltransfection efficiency, improved persistence of the vector in skincells (both through improved replication or through avoidance ofdestruction by immune cells), and improved antigen expression in skincells, and improved induction of an immune response.

Methods of Reassembly (Optionally in Combination with Other DirectedEvolution Methods Described Herein), Selection, and Screening

These methods involve performing stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly using as substrates plasmid, naked DNA vectors, or viralvector nucleic acids, including, for example, adenoviral vectors.Libraries of experimentally evolved (e.g. by polynucleotide reassembly&/or polynucleotide site-saturation mutagenesis) nucleic acids arescreened to identify those nucleic acids that confer upon a vector anenhanced ability to induce an immune response upon topicaladministration. Screening can be conducted by, for example, topicallyapplying a library of experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis) vectors toskin, either mouse skin, monkey skin, or human skin that has beentransplanted to immunodeficient mice, or to normal human skin in vivo.Vectors that persist and/or provide efficient and long-lastingexpression of marker gene are recovered from the skin samples. In apreferred embodiment, the desired cells are first selected by cellsorting, magnetic beads, or panning. For example, recovery can beeffected through expression of a marker gene (e.g., GFP) and detectingcells that are transfected using fluorescence microscopy or flowcytometry. Cells that express the marker gene can be isolated using flowcytometry based cell sorting. Screening can also involve selection ofvectors that induce the highest specific antibody or CTL responses uponadministration to a test mammal, or the identification of vectors thatprovide an enhanced protective immune response to challenge with acorresponding pathogen. Experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis)polynucleotides are then recovered, e.g., by polymerase chain reaction,or the entire vectors can be purified from these selected cells. Ifdesired, further optimization of topical application efficiency can beobtained by subjecting the recovered experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) polynucleotides to new rounds of reassembly (optionally incombination with other directed evolution methods described herein) andselection.

Administration of Genetic Vaccine Vectors Optimized for TopicalApplication

Genetic vaccine vectors that are optimized for topical application canbe applied topically to the skin, or by intramuscular, intravenous,intradermal, oral, anal, or vaginal delivery. The vector can bedelivered in any of the suitable forms that are known to those of skillin the art, such as a patch, a cream, as naked DNA, or as a mixture ofDNA and one or more transfection-enhancing agents such as liposomesand/or lipids. In preferred embodiments, the genetic vaccine vector isapplied after the skin or other target is rendered more susceptible touptake of the vector by, for example, mechanical abrasion, removal ofhair (e.g., by treatment with a commercially available product such asNair™, Neet™, and the like). In one embodiment, the skin is pretreatedwith proteases or lipases to make it more susceptible to DNA delivery.In addition, the DNA can be mixed with the proteases or lipases toenhance gene transfer. Alternatively, a droplet containing the vectorand other vaccine components, if any, can simply be administered to theskin.

2.6.6.2. Enhanced Ability to Escape Host Immune System

Limitations of Host Immune Responses Directed Against the Viral VectorSometimes Even Before Target Cells are Entered

Immunogenicity is a particular concern with viral vectors, since a hostimmune response can prevent a virus from reaching its intended targetparticularly in repeated administrations. The efficacy of some viralvectors which are used for genetic vaccination and gene delivery islimited by host immune responses directed against the viral vector. Forexample, most individuals have preexisting antibodies againstadenovirus. Adenoviral vectors can sometimes induce strong immuneresponses which can destroy cells harboring adenoviral vectors or clearadenoviral vectors from the host even before target cells are entered.Cellular immune responses can also be induced against nonviral vectorsadministered in naked form or shielded with a coat such as liposomes.

Methods to Create Genetic Vaccine Vectors with Improved Ability to Avoidthe Humoral and Cellular Immune Systems

The invention provides methods to create genetic vaccine vectors thatcan escape immune responses that would otherwise be detrimental toobtaining the desired effect. These methods are useful for prolongingexpression and secretion of pathogen antigen or pharmaceutically usefulprotein by genetic vaccine vectors. Several strategies are provided bywhich one can improve a genetic vaccine vector's ability to avoid thehumoral (Ab) and cellular (CTL) immune systems. These strategies can beused in combination to obtain optimal avoidance such as may be requiredfor highly immunogenic vectors such as adenovirus.

Incorporating into Genetic Vaccines One or More Components that InhibitPeptide Transport and/or MHC Class I Expression in Order to Obtain ViralVectors that are Capable of Escaping a Host CTL Immune Response

In one embodiment, the invention provides methods of obtaining viralvectors that are capable of escaping a host CTL immune response. Thismethod can be used in conjunction with methods for obtaining geneticvaccine vectors that can escape the humoral response; the combination ofapproaches is often desirable, as different viral serotypes often haveCTL epitopes in common, suggesting that virus variants which are notrecognized by antibodies still are likely to be recognized by CTLs. Thisembodiment of the invention involves incorporating into genetic vaccinesone or more components that inhibit peptide transport and/or SIC class Iexpression. An essential element in the activation of cytotoxic Tlymphocyte (CTL) responses is an interaction between T cell receptors onCTLs and antigenic peptide-MHC class I molecule complexes on antigenpresenting cells. Expression of MHC class I molecules on thymocytes andantigen presenting cells is a requirement for maturation and activationof antigen-specific CD8⁺ T lymphocytes. Thus, genes that encodeinhibitors of MHC class I-mediated antigen presentation can beexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) as described herein andplaced into viral vectors to obtain vectors that, when present in targetcells, do not induce destruction of the target cells by the cells of theimmune system. This can result in prolonged survival of cells harboringgenetic vaccine vectors, including those that express a pathogenantigen, as well as vectors that express a pharmaceutically usefulprotein. In the case of genetic vaccines, reduced expression of MHCclass I molecules will allow secretion of the pathogen antigen, whichthen will be presented by professional antigen presenting cellselsewhere. In the case of vectors encoding pharmaceutical proteins,reduced expression of MHC class I molecules prevents recognition by theimmune system prolonging the survival of the cells expressing the gene.

Reassembly (Optionally in Combination with Other Directed EvolutionMethods Described Herein) of Genes that Encode Inhibitors of TapActivity to Obtain Genes that Encode Optimized Tap Inhibitors

Among the proteins involved in MHC class I molecule expression andantigen presentation are those encoded by TAP genes (transportersassociated with antigen processing), which are described above. In oneembodiment of the invention, genes that encode inhibitors of TAPactivity are experimentally evolved (e.g. by polynucleotide reassembly&/or polynucleotide site-saturation mutagenesis) to obtain genes thatencode optimized TAP inhibitors. The substrates for these methods caninclude, for example, one or more of the viral genes that are known toregulate levels of MHC class I molecule expression. TAP 1 and TAP2 geneexpression is 5-10-fold and 100-fold reduced, respectively, in cellstransformed by adenovirus 12, which results in reduced class Iexpression and thus leads to reduced virus-specific cytotoxic Tlymphocyte responses. Similarly, TAP gene expression is downregulated in49% of HPV-16⁺ cervical carcinomas (Seliger et al. (1997) Immunol. Today18: 292). Thus, adenovirus and HPV viral nucleic acids provide examplesof suitable substrates for carrying out the methods of the invention.Additional examples of suitable stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly substrates for this embodiment of the invention include thehuman cytomegalovirus (CMV) encoded genes US2, US3 and US11, which candownregulate MHC class I expression (Wiertz et al. (1996) Nature 384:432 and Cell (1996) 84: 769; Ahn et al. (1996) Proc. Nat'l. Acad. Sci.USA 93: 10990). Another human CMV gene that encodes an inhibitor ofTAP-dependent peptide translocation is US6 (Lehner et al. (1997) Proc.Nat'l. Acad. Sci. USA 94: 6904-9). Cells transfected with US6 hadreduced expression of MHC class I molecules on their surface and reducedcapacity to activate cytotoxic T lymphocytes.

Reassembly (Optionally in Combination with Other Directed EvolutionMethods Described Herein) of this 7 kb Cluster of Genes in Order to Findthe Most Potent Sequence for Inhibiting the Expression of MHC Class IMolecules, which can Also be Used for Generation of Animal Models

Thus, in one embodiment, the invention involves stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly of this cluster of genes (approximately 7 kb),or fragments thereof, in order to identify the sequences that are mostpotent in inhibiting the expression of MHC class I molecules. Suchoptimized TAP inhibitor polynucleotide sequences are useful not only foruse in constructing vectors that can escape CTL immune responses, butalso for generation of animal models for use with human viruses thatnormally are eliminated in laboratory animals due to theirimmunogenicity. The desired expression levels and functional propertiesof TAP inhibitors may vary depending on whether genetic vaccine vector,gene therapy vector or animal model is evolved.

Reassembly (Optionally in Combination with Other Directed EvolutionMethods Described Herein) of Other Genes Involved in DownregulatingExpression of MHC Class I Molecules and/or Antigen Presentation

Alternative embodiments of the invention involve stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly of other genes that are involved indownregulating expression of MHC class I molecules and/or antigenpresentation. Examples of other possible target genes include genesencoding adenoviral E3 protein, herpes simplex ICP47 protein, andtapasin antagonists (Seliger et al. (1997) Immunol. Today 18:292-299;Galoncha et al. (1997) J Exp. Med. 185: 1565-1572; Li et al. (1997)Proc. Nat'l. Acad. Sci. USA 94: 8708-8713; Ortmann et al. (1997) Science277: 1306-1309.

A Gene that Encodes an MHC-Like Molecule that Inhibits NK Cell Functionbut is Unable to Present Antigens to T Lymphocytes

Because reduced expression of MHC class I molecules on cell surfaces mayact as a stimulus for NK cells, it may be useful to include in geneticvaccine vectors a gene that encodes an MHC like molecule that inhibitsNK cell function but is unable to present antigens to T lymphocytes. Anexample of such molecule is MHC class I homologue encoded bycytomegalovirus (Farrell et al. (1997) Nature 3 86: 510-514).

Obtaining Viral Vectors that Exhibit an Enhanced Capability of AvoidingAttack by CD4+ T Lymphocytes

The invention also provides methods of obtaining viral vectors thatexhibit an enhanced capability of avoiding attack by CD4⁺ T lymphocytes.Such vectors are particularly useful in situations where the targetcells are capable of expressing MHC class II molecules, such as in thecase of vaccinations and gene therapy targeted to the cells of theimmune system. Substrates for stochastic (e.g. polynucleotide shuffling& interrupted synthesis) and non-stochastic polynucleotide reassemblyinclude genes that encode inhibitors of MHC class II molecules such as,for example, IL-10 and antagonists of IFN-γ (such as soluble IFN-γreceptor).

Improving Sequences that Result in Inhibition of MHC Class I Expression,MHC Class II Expression, and Additional Sequences that Encode Homologsof MHC Class I Molecules

Vectors that have the greatest capability of escaping the host immunesystem, will typically include DNA sequences that result in inhibitionof MHC class I expression and MHC class II expression, and additionalsequences that encode homologs of MHC class I molecules. The propertiesof all these can be further improved by stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly according to the methods of the invention.

Methods for Screening the Library to Identify Those Polynucleotides thatExhibit the Desired Effect on the Host Immune Response

Once a library of experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis) DNAmolecules is obtained, any of several methods are available forscreening the library to identify those polynucleotides that, whenpresent in a viral vector (or in an animal model) exhibit the desiredeffect on the host immune response. For example, to obtainexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) polynucleotides that inhibitMHC class I expression and/or antigen presentation, a library ofexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) genes can be incorporatedinto genetic vaccine or gene therapy vectors and transfected into humancell lines, such as, for example, HeLa, U937 or Jijoye, in a single tubetransfection. Primary human monocytes, or dendritic cells generated byculturing human cord blood cells or monocytes in the presence of IL-4and GM-CSF, are also suitable. Initial screening can be done usingFACS-sorting.

Cells Expressing the Lowest Levels of MHC Class I Molecules are Expectedto have the Lowest Capacity to Induce CTL Responses

Cells expressing the lowest levels of MHC class I molecules areselected, the polynucleotides that encode the MHC inhibitors, or wholeplasmids containing the sequences, are recovered. If desired, theselected sequences can be subjected to new rounds of reassembly(optionally in combination with other directed evolution methodsdescribed herein) and selection. Cells expressing the lowest levels ofMHC class I molecules are expected to have the lowest capacity to induceCTL responses.

Screening Method: Infecting Library of Experimentally Evolved (e.g. byPolynucleotide Reassembly &/or Polynucleotide Site-SaturationMutagenesis) Polynucleotides that Encode Inhibitors of MHC Class IExpression Incorporated into HPV Vectors

Another screening method involves incorporating libraries ofexperimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation) polynucleotides that encode inhibitorsof MHC class I expression into human papillomavirus (HPV) vectors. Thislibrary is injected into the skin of mice.

Normally Murine Cells Expressing HPV are Destroyed by the Host ImmuneSystem. Cells Expressing Potent Inhibitors of Peptide Transportationand/or MHC Class Expression Will be Able to Escape the Immune Response

However, cells expressing potent inhibitors of peptide transportationand/or MHC class expression will be able to escape the immune response.The cells that express a marker gene present on the vector, such as GFP,for extended periods of time are selected, the sequences or wholeplasmids are recovered, and, if further optimization is desired, theselected sequences are subjected to new rounds of reassembly (optionallyin combination with other directed evolution methods described herein)and selection. Long-lasting maintenance of HPV in mice will allow drugscreening and vaccine studies, which to date have not been possible dueto high immunogenicity of HPV in mice.

Evolved Inhibitors Will Block Efficient Presentation of ImmunogenicPeptides, and Hence, Will Strongly Downregulate Activation ofAntigen-Specific CTLs Allowing Long-Lasting Transgene Expression In Vivo

In another embodiment, the libraries of experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) polynucleotides encoding inhibitors of MHC class Iexpression are incorporated into human adenovirus vectors. This libraryis transfected into human cell lines, such as HeLa cells, and cellsexpressing the lowest levels of MHC class I molecules are selected asdescribed above. The sequences that provide the lowest levels of MHCclass I expression are further tested by analyzing the capacity ofantigen-presenting cells transfected with adenovirus harboring evolvedinhibitors of MHC class I expression to activate specific T cell linesor clones. These inhibitors will block efficient presentation ofimmunogenic peptides, and hence, will strongly downregulate activationof antigen-specific CTLs allowing long-lasting transgene expression invivo.

Methods to Screen for Inhibitors

Methods to screen for improved inhibitors of MHC class II expressioninclude detection of MHC class II molecules on the surface of the targetcells by fluorescent labeled specific monoclonal antibodies,fluorescence microscopy, and flow cytometry. In addition, the inhibitorscan be analyzed in functional assays by studying the capacity of theinhibitors to block activation of MHC class II restrictedantigen-specific CD4⁺ T lymphocytes. For example, one can determine thecapacity of the inhibitor to inhibit induction of CD4⁺ T cellproliferation induced by autologous antigen presenting cells, such asmonocytes, dendritic cells, B cells or EBV-transformed B cell lines,that harbor genes encoding the MHC class II inhibitor or have beentreated with supernatant containing the inhibitor.

2.6.6.3. Enhanced Antiviral Activity

Obtaining a Recombinant Viral Vector which has an Enhanced Ability toInduce an Antiviral Response in a Cell

The invention also provides methods of obtaining a recombinant viralvector which has an enhanced ability to induce an antiviral response ina cell. These methods can include the steps of:

(1) reassembling (&/or subjecting to one or more directed evolutionmethods described herein) at least first and second forms of a nucleicacid which comprise a viral vector, wherein the first and second formsdiffer from each other in two or more nucleotides, to produce a libraryof recombinant viral vectors;(2) transfecting the library of recombinant viral vectors into apopulation of mammalian cells;(3) staining the cells for the presence of Mx protein; and(4) isolating recombinant viral vectors from cells which stain positivefor Mx protein, wherein recombinant viral vectors from positive stainingcells exhibit enhanced ability to induce an antiviral response.

Stochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly is used to produce a library ofrecombinant viral vectors. The library is transfected into a populationof mammalian cells, which are then tested for ability to induce anantiviral response. One suitable test involves staining the cells forthe presence of Mx protein, which is produced by cells that areexhibiting an antiviral response (see, e.g., Hallimen et al. (1997)Pediatric Research 41: 647-650; Melen et al. (1994) J Biol. Chem. 269:2009-2015).

Recombinant viral vectors can be isolated from cells which stainpositive for Mx protein. These recombinant viral vectors from positivestaining cells are enriched for those that exhibit enhanced ability toinduce an antiviral response. Viral vectors for which this method isuseful include, for example, influenza virus.

2.6.6.4. Evolution of Vectors Having Increased Copy Number in ProductionCells

Desirability of Method to Increase the Plasmid Copy Number After AllElements have been Cloned in the Vector, Especially when the Plasmid isto be Manufactured on a Large Scale

The invention provides methods for obtaining vector components thathave, when present in a genetic vaccine vector (such as a plasmid) theability to replicate to a high copy number in a cell used to produce thevector. Plasmids can incorporate various heterologous DNA sequences,however the size or the nature of the cloned sequences in a givenplasmid vector may render that vector less able to grow to high copynumber in the bacteria in which it is propagated. It is thereforedesirable to have a method to increase the plasmid copy number after allelements have been cloned into the vector. This is especially importantwhen the plasmid is to be manufactured on a large scale as will be thecase for genetic vaccines.

Incorporating into the Plasmid One or More Polynucleotide Sequences thatBind Proteins which would Otherwise be Toxic to the Bacterium

The methods of the invention involve incorporating into the plasmid oneor more polynucleotide sequences that bind proteins which wouldotherwise be toxic to the bacterium. One suitable toxic moiety andbinding site combination is the transcription factor GATA-1 and itsrecognition site. It has been shown that expression of a DNA-bindingfragment of GATA-1 is toxic to bacteria; this toxicity apparentlyresults from inhibition of bacterial DNA replication. Trudel et al.((1996) Biotechniques 20: 684-693) have described a plasmid (pGATA) thatexpresses the Z2B2 region of GATA-1 as a GST fusion protein. Theexpression of the fusion protein in this plasmid is under the control ofthe IPTG-inducible lac promoter. The GST-GATA-1 fragment also bindsstrongly to a sequence from the mouse β-globin gene promoter as well asto the C-oligonucleotide from the β-globin gene 3′ enhancer; either orboth of these are suitable for use as binding sites in the methods ofthe invention.

Including Only a Single Form of the Selectable Marker in the ShufflingReaction to Achieve Significant Diversity in the Experimentally Evolved(e.g. by Polynucleotide Reassembly &/or Polynucleotide Site-SaturationMutagenesis) Library to Recover a Plasmid which is Improved in itsGrowth Properties while Fully Retaining the Appropriate SelectionFunction of the Plasmid

The plasmids preferably also include a selectable marker such as, forexample, kanamycin resistance (aminoglycoside 3′-phosphotransferase (EC2.7.1.95)) and the like. The plasmid backbone polynucleotide sequence issubjected to stochastic (e.g. polynucleotide shuffling & interruptedsynthesis) and non-stochastic polynucleotide reassembly as describedherein to generate a library of plasmids which have different backbonesequences and possibly different supercoil densities. In order tointroduce sufficient sequence diversity to search for improved function,it is preferable to perform family stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly. This can be accomplished in the context of the presentinvention by including in the reassembly (optionally in combination withother directed evolution methods described herein) reaction(s) only asingle form of the selectable marker. In this way, significant diversitycan be achieved in the experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis) library torecover a plasmid which is improved in its growth properties while fullyretaining the appropriate selection function of the plasmid.

Selecting for High Copy Number Plasmids

The selection for high copy number plasmids is performed by introducingthe library of experimentally evolved (e.g. by polynucleotide reassembly&/or polynucleotide site-saturation mutagenesis) recombinant plasmidsinto the desired host cell. The host cells also express the toxicmoiety, preferably under the control of a promoter which is inducible.For example, the pGATA plasmid is suitable for use in E. coli hostcells. The experimentally evolved (e.g. by polynucleotide reassembly&/or polynucleotide site-saturation mutagenesis) plasmids are introducedinto the cells under non-inducing conditions. Transformed cells are thenplaced under conditions which induce expression of the toxic moiety. Forexample, E. coli cells that contain pGATA can be placed on mediacontaining increasing concentrations of IPTG Those target plasmids whichgrow to high copy number in the bacteria will express correspondinglyhigher numbers of the binding sequences for GATA-1. The target plasmidswill bind the GST-GATA-1 fusion protein and thus neutralize the toxiceffects on the bacteria.

Plasmids with the highest copy number are detected as those which conferthe best growth to bacteria on the inducer-containing growth media. Suchplasmids can be recovered and transformed into bacteria which lack thegene that encodes the toxic moiety; these plasmids should retain theirhigh copy number characteristics. Further rounds of reassembly(optionally in combination with other directed evolution methodsdescribed herein) can be used to isolate high copy number plasmids bythe above selection procedure. Alternatively, manual screening can bedone in the bacterial host of choice, lacking the toxic moiety-encodingplasmid, to avoid any effects due to the presence of this extraneousplasmid.

2.7. Optimization of Transport and Presentation of Antigens

The invention also provides methods of obtaining genetic vaccines andaccessory molecules that can improve the transport and presentation ofantigenic peptides. A library of experimentally generatedpolynucleotides is created and screened to identify those that encodemolecules that have improved properties compared to the wild-typecounterparts. The polynucleotides themselves can be used in geneticvaccines, or the gene products of the polynucleotides can be utilizedfor therapeutic or prophylactic applications.

2.7.1. Proteasomes

The class I peptides presented on major histocompatibility complexmolecules are generated by cellular proteasomes. Interferon-gamma canstimulate antigen presentation, and part of the mechanism of action ofinterferon may be due to induction of the proteasome beta-subunits LMP2and LMP7, which replace the homologous beta-subunits Y (delta) and X(epsilon). Such a replacement changes the peptide cleavage specificityof the proteasome and can enhance class I epitope immunogenicity. The Y(delta) and X (epsilon) subunits, as well as other recently discoveredproteasome subunits such as the MECL-1 homologue MC14, arecharacteristic of cells which are not specialized in antigenpresentation. Thus, the incorporation into cells by DNA transfer ofLMP2, LMP7, MECL-1 and/or other epitope presentation-specific andpotentially interferon-inducible subunits can enhance epitopepresentation. It is likely that the peptides generated by the proteasomecontaining the interferon-inducible subunits are transported to theendoplasmic reticulum by the TAP molecules.

The invention provides methods of obtaining proteasomes that exhibitincreased or decreased ability to specifically process MHC class Iepitopes. According to the methods, stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly is used to obtain evolved proteins that can either have newspecificities which might enhance the immunogenicity of some proteinsand/or enhance the activity of the subunits once they are bound to theproteasome. Because the transition from a non-specific proteasome to aclass I epitope-specific proteasome can pass through several states (inwhich some but not all of the interferon-inducible subunits areassociated with the proteasome), many different proteolyticspecificities can potentially be achieved. Evolving the specificLMP-like subunits can therefore create new proteasome compositions whichhave enhanced functionality for the presentation of epitopes.

The methods involve performing stochastic (e.g. polynucleotide shuffling& interrupted synthesis) and non-stochastic polynucleotide reassemblyusing as substrates two or more forms of polynucleotides which encodeproteasome components, where the forms of polynucleotides differ in atleast one nucleotide. Reassembly (optionally in combination with otherdirected evolution methods described herein) is performed as describedherein, using polynucleotides that encode any one or more of the variousproteasome components, including, for example, LMP2, LMP7, MECL-1 andother individual proteasome components that are specifically involved inclass I epitope presentation. Examples of suitable substrates aredescribed in, e.g., Stoliwasser et al. (1997) Eur. J Immunol. 27:1182-1187 and Gaczynska et al. (1996) J Biol. Chem. 271: 17275-17280. Ina preferred embodiment, polynucleotide reassembly (optionally incombination with other directed evolution methods described herein) isused, in which the different substrates are proteasomecomponent-encoding polynucleotides from different species.

After the reassembly (&/or one or more additional directed evolutionmethods described herein) reaction is completed, the resulting libraryof experimentally generated polynucleotides is screened to identifythose which encode proteasome components having the desired effect onclass I epitope production. For example, the experimentally generatedpolynucleotides can be introduced into a genetic vaccine vector whichalso encodes a particular antigen of interest. The library of vectorscan then be introduced into mammalian cells which are then screened toidentify cells which exhibit increased antigen-specific immunogenicity.Methods of analyzing proteasome activity are described in, for example,Groettrup et al. (1997) Proc. Nat'l. Acad. Sci. USA 94: 8970-8975 andGroettrup et al. (1997) Eur. J. Immunol. 26: 863-869.

Alternatively, one can use the methods of the invention to evolveproteins which bind strongly to the proteasome but have decreased or noactivity, thus antagonizing the proteasome activity and diminishing acells ability to present class I molecules. Such molecules can beapplied to gene therapy protocols in which it is desirable to lower theimmunogenicity of exogenous proteins expressed in the cells as a resultof the gene therapy, and which would otherwise be processed for class Ipresentation allowing the cell to be recognized by the immune system.Such high-affinity low-activity LMP-like subunits will demonstrateimmuno suppressive effects which are also of use in other therapeuticprotocols where cells expressing a non-self protein need to be protectedfrom an immune response.

The specificity of the proteasome and the TAP molecules (discussedbelow) may have co-evolved naturally. Thus it may be important that thetwo pathways of the class I processing system be functionally matched. Afurther aspect of the invention involves performing stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly simultaneously on the two gene familiesfollowed by random combinations of the two in order to discoverappropriate matched proteolytic and transport specificities.

2.7.2. Antigen Transport

The invention provides methods of improving transport of antigenicpeptides from the cytosolic compartment to the endoplasmic reticulum andthereby to the cell surface in the context of MHC class I molecules.Enhanced expression of antigenic peptides results in enhanced immuneresponse, particularly in improved activation of CD8⁺ cytotoxiclymphocytes. This is useful in the development of DNA vaccines and ingene therapy.

In one embodiment, the invention involves evolving TAP-genes(transporters associated with antigen processing) to obtain genes thatexhibit improved antigen presentation. TAP genes are members ofATP-binding cassette family of membrane translocators. These proteinstransport antigenic peptides to MHC class I molecules and are involvedin the expression and stability of MEC class I molecules on the cellsurface. Two TAP genes, TAP1 and TAP2, have been cloned to date (Powiset al. (1996) Proc. Nat'l. Acad. Sci. USA 89: 1463-1467; Koopman et al.(1997) Curr. Opin. Immunol. 9: 80-88; Monaco (1995) J Leukocyte Biol.57: 543-57). TAP1 and TAP2 form a heterodimer and these genes arerequired for transport of peptides into the endoplasmic reticulum, wherethey bind to MHC class I molecules. The essential role of TAP geneproducts in presentation of antigenic peptides was demonstrated in micewith disrupted TAP genes. TAP1-deficient mice have drastically reducedlevels of surface expression of MHC class I, and positive selection ofCD8⁺ T cells in the thymus is strongly reduced. Therefore, the number ofCD8⁺ T lymphocytes in the periphery of TAP-deficient mice is extremelylow. Transfection of TAP genes back into these cells restores the levelof MHC class I expression.

TAP genes are a good target for polynucleotide (e.g. gene, promoter,enhancer, intron, & the like) reassembly (optionally in combination withother directed evolution methods described herein) because of naturalpolymorphism and because these genes of several mammalian species havebeen cloned and sequenced, including human (Beck et al. (1992) J Mol.Biol. 228: 433-441; Genbank Accession No. Y13582; Powis et al., supra.),gorilla TAP1 (Laud et al. (1996) Human Immunol. 50: 91-102), mouse(Reiser et al. (1988) Proc. Nat'l. Acad. Sci. USA 85: 2255-2259;Marusina et al. (1997) J Immunol, 158: 5251-5256, TAP1: GenbankAccession Nos. U60018, U60019, U60020, U60021, U60022, andL76468-L67470; TAP2: Genbank Accession Nos. U60087, U60088, U6089,U60090, U60091 and U60092), hamster (TAP1, Genbank Accession Nos.AF001154 and AF001157; TAP2, Genbank Accession Nos. AF001156 andAF001155). Furthermore, it has been shown that point mutations in TAPgenes may result in altered peptide specificity and peptidepresentation. Also, functional differences in TAP genes derived fromdifferent species have been observed. For example, human TAP and rat TAPcontaining the rTA.P2a allele are rather promiscuous, whereas mouse TAPis restrictive and select against peptides with C-terminal smallpolar/hydrophobic or positively charged amino acids. The basis for thisselectivity is unknown.

The methods of the invention involve performing stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly of TAP1 and TAP2 genes using as substrates atleast two forms of TAP1 and/or TAP2 polynucleotide sequences whichdiffer in at least one nucleotide position. In a preferred embodiment,TAP sequences derived from several mammalian species are used as thesubstrates for reassembly (optionally in combination with other directedevolution methods described herein).

Natural polymorphism of the genes can provide additional diversity ofsubstrate. If desired, optimized TAP genes obtained from one round ofreassembly (optionally in combination with other directed evolutionmethods described herein) and screening can be subjected to additionalreassembly (optionally in combination with other directed evolutionmethods described herein)/screening rounds to obtain further optimizedTAP-encoding polynucleotides.

To identify optimized TAP-encoding polynucleotides from a library ofrecombinant TAP genes, the genes can be expressed on the same plasmid asa target antigen of interest. If this step is limiting the extent ofantigen presentation, then enhanced presentation to CD8⁺ CTL willresult. Mutants of TAPs may act selectively to increase expression of aparticular antigen peptide fragment for which levels of expression areotherwise limiting, or to cause transport of a peptide that wouldnormally never be transferred into the RER and made available to bind toMHC Class I.

When used in the context of gene therapy vectors in cancer treatment,evolved TAP genes provide a means to enhance expression of MHC class Imolecules on tumor cells and obtain efficient presentation of antigenictumor-specific peptides. Thus, vectors that contain the evolved TAPgenes can induce potent immune responses against the malignant cells.Experimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) TAP genes can be transfectedinto malignant cell lines that express low levels of MHC class Imolecules using retroviral vectors or electroporation.

Transfection efficiency can be monitored using marker genes, such asgreen fluorescent protein, encoded by the same vector as the TAP genes.Cells expressing equal levels of green fluorescent protein but thehighest levels of MHC class I molecules, as a marker of efficient TAPgenes, are then sorted using flow cytometry, and the evolved TAP genesare then recovered from these cells by, for example, PCR or byrecovering the entire vectors.

These sequences can then subjected into new rounds of reassembly(optionally in combination with other directed evolution methodsdescribed herein), selection and recovery, if further optimization isdesired. Molecular evolution of TAP genes can be combined withsimultaneous evolution of the desired antigen. Simultaneous evolution ofthe desired antigen can further improve the efficacy of presentation ofantigenic peptides following DNA vaccination. The antigen can beevolved, using polynucleotide reassembly (optionally in combination withother directed evolution methods described herein), to containstructures that allow optimal presentation of desired antigenic peptideswhen optimal TAP genes are expressed. TAP genes that are optimal forpresentation of antigenic peptides of one given antigen may be differentfrom TAP genes that are optimal for presentation of antigenic peptide ofanother antigen. Polynucleotide (e.g. gene, promoter, enhancer, intron,& the like) reassembly (optionally in combination with other directedevolution methods described herein) technique is ideal, and perhaps theonly, method to solve this type of problem. Efficient presentation ofdesired antigenic peptides can be analyzed using specific cytotoxic Tlymphocytes, for example, by measuring the cytokine production or CTLactivity of the T lymphocytes using methods known to those of skill inthe art.

2.7.3. Cytotoxic T-cell Inducing Sequences and Immunogenic AgonistSequences

Certain proteins are better able than others to carry MHC class Iepitopes because they are more readily used by the cellular machineryinvolved in the necessary processing for class I epitope presentation.The invention provides methods of identifying expressed polypeptidesthat are particularly efficient in traversing the various biosyntheticand degradative steps leading to class I epitope presentation and theuse of these polypeptides to enhance presentation of CTL epitopes fromother proteins.

In one embodiment, the invention provides Cytotoxic T-cell InducingSequences (CTIS), which can be used to carry heterologous class Iepitopes for the purpose of vaccinating against the pathogen from whichthe heterologous epitopes are derived. One example of a CTIS is obtainedfrom the hepatitis B surface antigen (HBsAg), which has been shown to bean effective carrier for its own CTL epitopes when delivered as aprotein under certain conditions. DNA immunization with plasmidsexpressing the HBsAg also induces high levels of CTL activity. Theinvention provides a shorter, truncated fragment of the HBsAgpolypeptide which functions very efficiently in inducing CTL activity,and attains CTL induction levels that are higher than with the HBsAgprotein or with the plasmids encoding the full-length HBsAg polypeptide.Synthesis of a CTIS derived from HBsAg is described in Example 3; and adiagram of a CTIS is shown, described &/or referenced herein (includingincorporated by reference).

The ER localization of the truncated polypeptide may be important inachieving suitable proteolytic liberation of the peptide(s) containingthe CTL epitopes (see Cresswell & Hughes (1997) Curr. Biol. 7:R552-R555; Craiu et al. (1997) Proc. Nat'l. Acad. Sei. USA 94:10850-10855). The preS2 region and the transmembrane region provideT-helper epitopes which may be important for the induction of a strongcytotoxic immune response. Because the truncated CTIS polypeptide has asimple structure, it is possible to attach one or more heterologousclass I epitope sequences to the C-terminal end of the polypeptidewithout having to maintain any specific protein conformation. Suchsequences are then available to the class I epitope processingmechanisms. The size of the polypeptide is not subject to the normalconstraints of the native HBsAg structure. Therefore the length of theheterologous sequence and thus the number of included CTL epitopes isflexible. This is shown schematically herein. The ability to include along sequence containing either multiple and distinct class I sequences,or alternatively different variations of a single CTL sequence, allowsstochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly methodology to be applied.

The invention also provides methods of obtaining Immunogenic AgonistSequences (IAS) which induce CTLs capable of specific lysis of cellsexpressing the natural epitope sequence. In some cases, the reactivityis greater than if the CTL response is induced by the natural epitope.Such IAS-induced CTL may be drawn from a T-cell repertoire differentfrom that induced by the natural sequence. In this way, poorresponsiveness to a given epitope can be overcome by recruiting T cellsfrom a larger pool. In order to discover such IAS, the amino acid ateach position of a CTL-inducing peptide (excluding perhaps the positionsof the so-called anchor residues) can be varied over the range of the 19amino acids not normally present at the position. Stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly methodology can be used to scan a large rangeof sequence possibilities.

A synthetic gene segment containing multiple copies of the originalepitope sequence can be prepared such that each copy possesses a smallnumber of nucleotide changes. The gene segment can be experimentallyevolved (e.g. by polynucleotide reassembly &/or polynucleotidesite-saturation mutagenesis) to create a diverse range of CTL epitopesequences, some of which should function as IAS. This process isillustrated herein.

In practice, oligonucleotides are typically constructed in accordancewith the above design and polymerized enzymatically to form thesynthetic gene segment of the concatenated epitopes. Restriction sitescan be incorporated into a fraction of the oligonucleotides to allow forcleavage and selection of given size ranges of the concatenatedepitopes, most of which will have different sequences and thus will bepotential IAS. The epitope-containing gene segment can be joined byappropriate cloning methods to a CTIS, such as that of HBsAg. Theresulting plasmid constructions can be used for DNA-based C immunizationand CTL induction.

2.8. Genetic Vaccine Pharmaceutical Compositions and Methods ofAdministration Using Genetic Vaccines in Prophylaxis and Therapy ofInfectious Diseases, Autoimmune Diseases, Other Inflammatory Conditions,Allergies, Asthma, and Cancer and the Prevention of Metastasis

The vector components and multicomponent genetic vaccines of theinvention are useful for treating and/or preventing various diseases andother conditions. For example, genetic vaccines that employ the reagentsobtained according to the methods of the invention are useful in bothprophylaxis and therapy of infectious diseases, including those causedby any bacterial, fungal, viral, or other pathogens of mammals. Thereagents obtained using the invention can also be used for treatment ofautoimmune diseases including, for example, rheumatoid arthritis, SLE,diabetes mellitus, myasthenia gravis, reactive arthritis, ankylosingspondylitis, and multiple sclerosis. These and other inflammatoryconditions, including IBD, psoriasis, pancreatitis, and variousimmunodeficiencies, can be treated using genetic vaccines that includevectors and other components obtained using the methods of theinvention. Genetic vaccine vectors and other reagents obtained using themethods of the invention can be used to treat allergies and asthma.Moreover, the use of genetic vaccines have great promise for thetreatment of cancer and prevention of metastasis. By inducing an immuneresponse against cancerous cells, the body's immune system can beenlisted to reduce or eliminate cancer.

Use of Recombinant Multivalent Antigens

The multivalent antigens of the invention are useful for treating and/orpreventing the various diseases and conditions with which the respectiveantigens are associated. For example, the multivalent antigens can beexpressed in a suitable host cell and are administered in polypeptideform. Suitable formulations and dosage regimes for vaccine delivery arewell known to those of skill in the art. The improved immunomodulatorypolynucleotides and polypeptides of the invention are useful fortreating and/or preventing the various diseases and conditions withwhich the respective antigens are associated.

An Antigen for a Particular Condition can be Optimized Using Reassembly(&/or One or More Additional Directed Evolution Methods DescribedHerein) and Selection Methods Analogous to Those Described Herein.

In presently preferred embodiments, the reagents obtained using theinvention (e.g. optimized experimentally generated polynucleotides thatencode improved allergens), are used in conjunction with a geneticvaccine. The choice of vector and components can also be optimized forthe particular purpose of treating allergy or other conditions. Inpresently preferred embodiments, the optimized genetic vaccinecomponents are used in conjunction with other optimized genetic vaccinereagents. For example, an antigen that is useful for a particularcondition can be optimized by methods analogous to the reassembly (&/orone or more additional directed evolution methods described herein) andscreening methods described herein.

The polynucleotide that encodes the recombinant antigenic polypeptidecan be placed under the control of a promoter, e.g., a high activity ortissue-specific promoter. The promoter used to express the antigenicpolypeptide can itself be optimized using reassembly (&/or one or moreadditional directed evolution methods described herein) and selectionmethods analogous to those described herein, as described inInternational Application No. PCT/US97/17300 (International PublicationNo. WO 98/13487).

The vector can contain immunostimulatory sequences such as are describedherein. A vector engineered to direct a T_(H)1 response is preferred formany of the immune responses mediated by the antigens described herein.The reagents obtained using the methods of the invention can also beused in conjunction with multicomponent genetic vaccines, which arecapable of tailoring an immune response as is most appropriate toachieve a desired effect. It is sometimes advantageous to employ agenetic vaccine that is targeted for a particular target cell type(e.g., an antigen presenting cell or an antigen processing cell);suitable targeting methods are described herein.

Delivery of Genetic Vaccines and Delivery Vehicles to Mammals In Vivoand Ex Vivo

Genetic vaccines, (e.g. genetic vaccines that include the optimizedexperimentally generated polynucleotides obtained as described herein,such as genetic vaccines that encode the multivalent antigens describedherein, including the multicomponent genetic vaccines described herein),can be delivered to a mammal (including humans) to induce a therapeuticor prophylactic immune response. Vaccine delivery vehicles can bedelivered in vivo by administration to an individual patient, typicallyby systemic administration (e.g., intravenous, intraperitoneal,intramuscular, subdermal, intracranial, anal, vaginal, oral, buccalroute or they can be inhaled) or they can be administered by topicalapplication.

Alternatively, vectors can be delivered to cells ex vivo, such as cellsexplanted from an individual patient (e.g., lymphocytes, bone marrowaspirates, tissue biopsy) or universal donor hematopoietic stem cells,followed by reimplantation of the cells into a patient, usually afterselection for cells which have incorporated the vector.

Delivery Methods and References

A large number of delivery methods are well known to those of skill inthe art. Such methods include, for example liposome-based gene delivery(Debs and Zhu (1993) WO 93/24640; Mannino and Gould-Fogerite (1988)BioTechniques 6(7): 682-691; Rose U.S. Pat. No. 5,279,833; Brigham(1991) WO 91/06309; and Felgner et al. (1987) Proc. Natl. Acad. Sci. USA84: 7413-7414), as well as use of viral vectors (e.g., adenoviral (see,e.g., Berns et al. (1995) Ann. NY Acad. Sci. 772: 95-104; Ali et al.(1994) Gene Ther. 1: 367-384; and Haddada et al. (1995) Curr. Top.Microbiol. Immunol. 199 (Pt 3): 297-306 for review), papillomaviral,retroviral (see, e.g., Buchscher et al. (1992) J Virol. 66(5) 2731-2739;Johann et al. (1992) J Virol. 66 (5):1635-1640 (1992); Sommerfelt etal., (1990) Virol. 176:58-59; Wilson et al. (1989) J Virol.63.2374-2378; Miller et al., J Virol. 65:2220-2224 (1991); Wong-Staal etal., PCT/US94/05700, and Rosenburg and Fauci (1993) in FundamentalImmunology, Third Edition Paul (ed) Raven Press, Ltd., New York and thereferences therein, and Yu et al., Gene Therapy (1994) supra.), andadeno-associated viral vectors (see, West et al. (1987) Virology160:38-47; Carter et al. (1989) U.S. Pat. No. 4,797,368; Carter et al.WO 93/24641 (1993); Kotin (1994) Human Gene Therapy 5:793-801; Muzyczka(1994) J Clin. Invst. 94:1351 and Samulski (supra) for an overview ofAAV vectors; see also, Lebkowski, U.S. Pat. No. 5,173,414; Tratschin etal. (1985) Mol. Cell. Biol. 5(11):3251-3260; Tratschin, et al. (1984)Mol. Cell. Biol., 4:2072-2081; Hermonat and Muzyczka (1984) Proc. Natl.Acad. Sci. USA, 81:6466-6470; McLaughlin et al. (1988) and Samulski etal. (1989) J Virol., 63:03 822-3 828), and the like.

Introduction of “Naked” DNA and/or RNA that Comprises a Genetic VaccineDirectly into a Tissue or Using “Biolistic” or Particle-MediatedTransformation, Both In Vivo and Ex Vivo

“Naked” DNA and/or RNA that comprises a genetic vaccine can beintroduced directly into a tissue, such as muscle. See, e.g., U.S. Pat.No. 5,580,859. Other methods such as “biolistic” or particle-mediatedtransformation (see, e.g., Sanford et al., U.S. Pat. No. 4,945,050; U.S.Pat. No. 5,036,006) are also suitable for introduction of geneticvaccines into cells of a mammal according to the invention. Thesemethods are useful not only for in vivo introduction of DNA into amammal, but also for ex vivo modification of cells for reintroductioninto a mammal. As for other methods of delivering genetic vaccines, ifnecessary, vaccine administration is repeated in order to maintain thedesired level of immunomodulation.

Methods of Administering Packaged Nucleic Acids in Mammals forTransduction of Cells In Vivo

Genetic vaccine vectors (e.g., adenoviruses, liposomes,papillomaviruses, retroviruses, etc.) can be administered directly tothe mammal for transduction of cells in vivo. The genetic vaccinesobtained using the methods of the invention can be formulated aspharmaceutical compositions for administration in any suitable manner,including parenteral (e.g., subcutaneous, intramuscular, intradermal, orintravenous), topical, oral, rectal, intrathecal, buccal (e.g.,sublingual), or local administration, such as by aerosol ortransdermally, for prophylactic and/or therapeutic treatment.Pretreatment of skin, for example, by use of hair-removing agents, maybe useful in transdermal delivery. Suitable methods of administeringsuch packaged nucleic acids are available and well known to those ofskill in the art, and, although more than one route can be used toadminister a particular composition, a particular route can oftenprovide a more immediate and more effective reaction than another route.

Pharmaceutically acceptable carriers are determined in part by theparticular composition being administered, as well as by the particularmethod used to administer the composition. Accordingly, there is a widevariety of suitable formulations of pharmaceutical compositions of thepresent invention. A variety of aqueous carriers can be used, e.g.,buffered saline and the like. These solutions are sterile and generallyfree of undesirable matter. These compositions may be sterilized byconventional, well known sterilization techniques. The compositions maycontain pharmaceutically acceptable auxiliary substances as required toapproximate physiological conditions such as pH adjusting and bufferingagents, toxicity adjusting agents and the like, for example, sodiumacetate, sodium chloride, potassium chloride, calcium chloride, sodiumlactate and the like. The concentration of genetic vaccine vector inthese formulations can vary widely, and will be selected primarily basedon fluid volumes, viscosities, body weight and the like in accordancewith the particular mode of administration selected and the patient'sneeds.

Formulations suitable for oral administration can consist of (a) liquidsolutions, such as an effective amount of the packaged nucleic acidsuspended in diluents, such as water, saline or PEG 400; (b) capsules,sachets or tablets, each containing a predetermined amount of the activeingredient, as liquids, solids, granules or gelatin; (c) suspensions inan appropriate liquid; and (d) suitable emulsions. Tablet forms caninclude one or more of lactose, sucrose, mannitol, sorbitol, calciumphosphates, corn starch, potato starch, tragacanth, microcrystallinecellulose, acacia, gelatin, colloidal silicon dioxide, croscannellosesodium, talc, magnesium stearate, stearic acid, and other excipients,colorants, fillers, binders, diluents, buffering agents, moisteningagents, preservatives, flavoring agents, dyes, disintegrating agents,and pharmaceutically compatible carriers.

Lozenge forms can comprise the active ingredient in a flavor, usuallysucrose and acacia or tragacanth, as well as pastilles comprising theactive ingredient in an inert base, such as gelatin and glycerin orsucrose and acacia emulsions, gels, and the like containing, in additionto the active ingredient, carriers known in the art. It is recognizedthat the genetic vaccines, when administered orally, must be protectedfrom digestion. This is typically accomplished either by complexing thevaccine vector with a composition to render it resistant to acidic andenzymatic hydrolysis or by packaging the vector in an appropriatelyresistant carrier such as a liposome. Means of protecting vectors fromdigestion are well known in the art. The pharmaceutical compositions canbe encapsulated, e.g., in liposomes, or in a formulation that providesfor slow release of the active ingredient.

The packaged nucleic acids, alone or in combination with other suitablecomponents, can be made into aerosol formulations (e.g., they can be“nebulized”) to be administered via inhalation. Aerosol formulations canbe placed into pressurized acceptable propellants, such asdichlorodifluoromethane, propane, nitrogen, and the like. Suitableformulations for rectal administration include, for example,suppositories, which consist of the packaged nucleic acid with asuppository base. Suitable suppository bases include natural orsynthetic triglycerides or paraffin hydrocarbons. In addition, it isalso possible to use gelatin rectal capsules which consist of acombination of the packaged nucleic acid with a base, including, forexample, liquid triglycerides, polyethylene glycols, and paraffinhydrocarbons.

Formulations suitable for parenteral administration, such as, forexample, by intraarticular (in the joints), intravenous, intramuscular,intradermal, intraperitoneal, and subcutaneous routes, include aqueousand non-aqueous, isotonic sterile injection solutions, which can containantioxidants, buffers, bacteriostats, and solutes that render theformulation isotonic with the blood of the intended recipient, andaqueous and non-aqueous sterile suspensions that can include suspendingagents, solubilizers, thickening agents, stabilizers, and preservatives.In the practice of this invention, compositions can be administered, forexample, by intravenous infusion, orally, topically, intraperitoneally,intravesically or intrathecally.

Parenteral Administration and Intravenous Administration are thePreferred Methods of Administration

The formulations of packaged nucleic acid can be presented in unit-doseor multi-dose sealed containers, such as ampoules and vials. Injectionsolutions and suspensions can be prepared from sterile powders,granules, and tablets of the kind previously described. Cells transducedby the packaged nucleic acid can also be administered intravenously orparenterally.

Dose Size

The dose administered to a patient, in the context of the presentinvention should be sufficient to effect a beneficial therapeuticresponse in the patient over time. The dose will be determined by theefficacy of the particular vector employed and the condition of thepatient, as well as the body weight or vascular surface area of thepatient to be treated. The size of the dose also will be determined bythe existence, nature, and extent of any adverse side-effects thataccompany the administration of a particular vector, or transduced celltype in a particular patient.

In determining the effective amount of the vector to be administered inthe treatment or prophylaxis of an infection or other condition, thephysician evaluates vector toxicities, progression of the disease, andthe production of anti-vector antibodies, if any. In general, the doseequivalent of a naked nucleic acid from a vector is from about 1 μg to 1mg for a typical 70 kilogram patient, and doses of vectors used todeliver the nucleic acid are calculated to yield an equivalent amount oftherapeutic nucleic acid. Administration can be accomplished via singleor divided doses.

In therapeutic applications, compositions are administered to a patientsuffering from a disease (e.g., an infectious disease or autoimmunedisorder) in an amount sufficient to cure or at least partially arrestthe disease and its complications. An amount adequate to accomplish thisis defined as a “therapeutically effective dose.” Amounts effective forthis use will depend upon the severity of the disease and the generalstate of the patient's health. Single or multiple administrations of thecompositions may be administered depending on the dosage and frequencyas required and tolerated by the patient. In any event, the compositionshould provide a sufficient quantity of the proteins of this inventionto effectively treat the patient.

In prophylactic applications, compositions are administered to a humanor other mammal to induce an immune response that can help protectagainst the establishment of an infectious disease or other condition.

Ability to Determine Toxicity Therapeutic Efficacy

The toxicity and therapeutic efficacy of the genetic vaccine vectorsprovided by the invention are determined using standard pharmaceuticalprocedures in cell cultures or experimental animals. One can determinethe LD₅₀ (the dose lethal to 50% of the population) and the ED₅₀ (thedose therapeutically effective in 50% of the population) usingprocedures presented herein and those otherwise known to those of skillin the art.

More on Dosage

A typical pharmaceutical composition for intravenous administrationwould be about 0.1 to 10 mg per patient per day. Dosages from 0.1 up toabout 100 mg per patient per day may be used, particularly when the drugis administered to a secluded site and not into the blood stream, suchas into a body cavity or into a lumen of an organ. Substantially higherdosages are possible in topical administration. Actual methods forpreparing parenterally administrable compositions will be known orapparent to those skilled in the art and are described in more detail insuch publications as Remington's Pharmaceutical Science, 15th ed., MackPublishing Company, Easton, Pa. (1980).

Packaging/Dispenser Devices

The genetic vaccines obtained using the methods of the invention (e.g.the multivalent antigenic polypeptides of the invention, and geneticvaccines that express the polypeptides) can be packaged in packs,dispenser devices, and kits for administering genetic vaccines to amammal. For example, packs or dispenser devices that contain one or moreunit dosage forms are provided. Typically, instructions foradministration of the compounds will be provided with the packaging,along with a suitable indication on the label that the compound issuitable for treatment of an indicated condition. For example, the labelmay state that the active compound within the packaging is useful fortreating a particular infectious disease, autoimmune disorder, tumor, orfor preventing or treating other diseases or conditions that aremediated by, or potentially susceptible to, a mammalian immune response.

2.9. Uses of Genetic Vaccines

Genetic vaccines which include optimized vector modules and otherreagents provided by the invention are useful for treating many diseasesand other conditions that are either mediated by a mammalian immunesystem or are susceptible to treatment by an appropriate immuneresponse. Representative examples of these diseases & antigensappropriate for each are listed below, described herein, or incorporatedby reference.

Substrates for Evolution of Optimized Recombinant Antigens

The invention provides methods of obtaining experimentally generatedpolynucleotides that encode antigens that exhibit improved ability toinduce an immune response to a pathogenic agent. The methods areapplicable to a wide range of pathogenic agents, including potentialbiological warfare agents and other organisms and polypeptides that cancause disease and toxicity in humans and other animals. The followingexamples are merely illustrative, and not limiting.

2.9.1. Infectious Diseases

Genetic vaccine vectors obtained according to the methods of theinvention are useful in both prophylaxis and therapy of infectiousdiseases, including those caused by any bacterial, fungal, viral, orother pathogens of mammals. In some embodiments, protection is conferredby use of a genetic vaccine vector that will express an antigen (eitheror both of a humoral antigen or a T cell antigen) of the pathogen ofinterest. In preferred embodiments, the antigen is evolved using themethods of the invention in order to obtain optimized antigens asdescribed herein. The vector induces an immune response against theantigen. One or several antigens or antigen fragments can be included inone genetic vaccine delivery vehicle. Examples of pathogens andcorresponding polypeptides from which an antigen can be obtainedinclude, but are not limited to, HIV (gp120, gp160), hepatitis B, C, D,E (surface antigen), rabies (glycoprotein), Schistosoma mansoni(calpain; Jankovic (1996) J Immunol. 157: 806-14). Other pathogeninfections that are treatable using genetic vaccine vectors include, forexample, herpes zoster, herpes simplex-1 and -2, tuberculosis (includingchronic, drug-resistant), lyme disease (Borrelia burgorferii), syphilis,parvovirus, rabies, human papillomavirus, and the like.

2.9.1.1 Bacterial Pathogens and Toxins

In some embodiments, the methods of the invention are applied tobacterial pathogens, as well as to toxins produced by bacteria and otherorganisms. One can use the methods to obtain experimentally generatedpolypeptides that can induce an immune response against the pathogen, aswell as recombinant toxins that are less toxic than native toxinpolypeptides. Often, the polynucleotides of interest encode polypeptidesthat are present on the surface of the pathogenic organism. Among thepathogens for which the methods of the invention are useful forproducing protective immunogenic experimentally generated polypeptidesare the Yersinia species.

Yersinia pestis, the causative agent of plague, is one of the mostvirulent bacteria known with LD₅₀ values in mouse of less than 10bacteria. The pneumonic form of the disease is readily spread betweenhumans by aerosol or infectious droplets and can be lethal within days.A particularly preferred target for obtaining a experimentally generatedpolypeptide that can protect against Yersinia infection is the Vantigen, which is a 37 kDa virulence factor, induces protective immuneresponses and is currently being evaluated as a subunit vaccine(Brubaker (1991) Current Investigations of the Microbiology of Yersinae,12: 127). The V-antigen alone is not toxic, but Y. pestis isolates thatlack the V-antigen are avirulent. The Yersinia V-antigen has beensuccessfully produced in E. coli by several groups (Leary et al. (1995)Infect. Immun. 3: 2854). Antibodies that recognize the V-antigen canprovide passive protection against homologous strains, but not againstheterologous strains. Similarly, immunization with purified V antigenprotects against only homologous strains. To obtain cross-protectiverecombinant V antigen, in a preferred embodiment, V antigen genes fromvarious Yersinia species are subjected to polynucleotide reassembly(optionally in combination with other directed evolution methodsdescribed herein). The genes encoding the V antigen from Y. pestis, Y.enterocolitica, and Y. pseudotuberculosis, for example, are 92-99%identical at the DNA level, making them ideal for optimization usingfamily reassembly (optionally in combination with other directedevolution methods described herein) according to the methods of theinvention. After reassembly (optionally in combination with otherdirected evolution methods described herein), the library of recombinantnucleic acids is screened and/or selected for those that encoderecombinant V antigen polypeptides that can induce an improved immuneresponse and/or have greater cross-protectivity.

Bacillus anthracis, the causative agent of anthrax, is another exampleof a bacterial target against which the methods of the invention areuseful. The anthrax protective antigen (PA) provides protective immuneresponses in test animals, and antibodies against PA also provide someprotection. However, the immunogenicity of PA is relatively poor, somultiple injections are typically required when wild-type PA is used.Co-vaccination with lethal factor (LF) can improve the efficacy ofwild-type PA vaccines, but toxicity is a limiting factor. Accordinglythe stochastic (e.g. polynucleotide shuffling & interrupted synthesis)and non-stochastic polynucleotide reassembly and antigen libraryimmunization methods of the invention can be used to obtain nontoxic LF.Polynucleotides that encode LF from various B. anthracis strains aresubjected to family reassembly (optionally in combination with otherdirected evolution methods described herein). The resulting library ofrecombinant LF nucleic acids can then be screened to identify those thatencode recombinant LF polypeptides that exhibit reduced toxicity. Forexample, one can inoculate tissue culture cells with the recombinant LFpolypeptides in the presence of PA and select those clones for which thecells survive. If desired, one can then backcross the nontoxic LFpolypeptides to retain the immunogenic epitopes of LF. Those that areselected through the first screen can then be subjected to a secondaryscreen. For example, one can test for the ability of the recombinantnontoxic LF polypeptides to induce an immune response (e.g., CTL orantibody response) in a test animal such as mice. In preferredembodiments, the recombinant nontoxic LF polypeptides are then testedfor ability to induce protective immunity in test animals againstchallenge by different strains of B. anthracis.

The protective antigen (PA) of B. anthracis is also a suitable targetfor the methods of the invention. PA-encoding nucleic acids from variousstrains of B. anthracis are subjected to stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly. One can then screen for proper folding in, for example, E.coli, using polyclonal antibodies. Screening for ability to inducebroad-spectrum antibodies in a test animal is also typically used,either alone or in addition to a preliminary screening method. Inpresently preferred embodiments, those experimentally generatedpolynucleotides that exhibit the desired properties can be backcrossedso that the immunogenic epitopes are maintained. Finally, the selectedrecombinants are tested for ability to induce protective immunityagainst different strains of B. anthracis in a test animal.

The Staphylococcus aureus and Streptococcus toxins are another exampleof a target polypeptide that can be altered using the methods of theinvention. Strains of Staphylococcus aureus and group A Streptococci areinvolved in a range of diseases, including food poisoning, toxic shocksyndrome, scarlet fever and various autoimmune disorders. They secrete avariety of toxins, which include at least five cytolytic toxins, acoagulase, and a variety of enterotoxins. The enterotoxins areclassified as superantigens in that they crosslink MHC class IImolecules with T cell receptors to cause a constitutive T cellactivation (Fields et al. (1996) Nature 384: 188). This results in theaccumulation of pathogenic levels of cytokines that can lead to multipleorgan failure and death. At least thirty related, yet distinctenterotoxins have been sequenced and can be phylogenetically groupedinto families. Crystal structures have been obtained for several membersalone and in complex with MHC class II molecules. Certain mutations inthe MHC class II binding site of the toxins strongly reduce theirtoxicity and can form the basis of attenuated vaccines (Woody et al.(1997) Vaccine 15: 133). However, a successful immune response to onetype of toxin may provide protection against closely related familymembers, whereas little protection against toxins from the otherfamilies is observed. Family reassembly (optionally in combination withother directed evolution methods described herein) of enterotoxin genesfrom various family members can be used to obtain recombinant toxinmolecules that have reduced toxicity and can induce a cross-protectiveimmune response. Experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis) antigens canalso be screened to identify antigens that elicit neutralizingantibodies in an appropriate animal model such as mouse or monkey.Examples of such assays can include ELISA formats in which the elicitedantibodies prevent binding of the enterotoxin to the MHC complex and/orT cell receptors on cells or purified forms. These assays can alsoinclude formats where the added antibodies would prevent T cells frombeing cross-linked to appropriate antigen presenting cells.

Cholera is an ancient, potentially lethal disease caused by thebacterium Vibrio cholerae and an effective vaccine for its prevention isstill unavailable. Much of the pathogenesis of this disease is caused bythe cholera enterotoxin. Ingestion of microgram quantities of choleratoxin can induce severe diarrhea causing loss of tens of liters offluid.

Cholera toxin is a complex of a single catalytic A subunit with apentameric ring of identical B subunits. Each subunit is inactive on itsown. The B subunits bind to specific ganglioside receptors on thesurface of intestinal epithelial cells and trigger the entry of the Asubunit into the cell. The A subunit ADP-ribosylates a regulatory Gprotein initiating a cascade of events causing a massive, sustained flowof electrolytes and water into the intestinal lumen resulting in extremediarrhea.

The B subunit of cholera toxin is an attractive vaccine target for anumber of reasons. It is a major target of protective antibodiesgenerated during cholera infection and contains the epitopes forantitoxin neutralizing antibodies. It is nontoxic without the A subunit,is orally effective, and stimulates production of a strong IgA-dominatedgut mucosal immune response, which is essential in protection againstcholera and cholera toxin. The B subunit is also being investigated foruse as an adjuvant in other vaccine preparations, and therefore, evolvedtoxins may provide general improvements for a variety of differentvaccines. The heat-labile enterotoxins (LT) from enterotoxigenic E. colistrains are structurally related to cholera toxin and are 75% identicalat the DNA sequence level. To obtain optimized recombinant toxinmolecules that exhibit reduced toxicity and increased ability to inducean immune response that is protective against V. cholerae and E. coli,the genes that encode the related toxins are subjected to stochastic(e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly.

The recombinant toxins are then tested for one or more of a severaldesirable traits. For example, one can screen for improvedcross-reactivity of antibodies raised against the recombinant toxinpolypeptides, for lack of toxicity in a cell culture assay, and forability to induce a protective immune response against the pathogensand/or against the toxins themselves. The experimentally evolved (e.g.by polynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) clones can be selected by phage display and/or screened byphage ELISA and ELISA assays for the presence of epitopes from thedifferent serotypes. Variant proteins with multiple epitopes can then bepurified and used to immunize mice or other test animal. The animalserum is then assayed for antibodies to the different B chain subtypesand variants that elicit a broad cross-reactive response will beevaluated further in a virulent challenge model. The E. coli and V.cholerae toxins can also act as adjuvants that are capable of enhancingmucosal immunity and oral delivery of vaccines and proteins.

Accordingly, One can Test the Library of Recombinant Toxins forEnhancement of the Adjuvant Activity

Experimentally evolved (e.g. by polynucleotide reassembly &/orpolynucleotide site-saturation mutagenesis) antigens can also bescreened for improved expression levels and stability of the B chainpentamer, which may be less stable than when in the presence of the Achain in the hexameric complex. Addition of a heat treatment step ordenaturing agents such as salts, urea, and/or guanidine hydrochloridecan be included prior to ELISA assays to measure yields of correctlyfolded molecules by appropriate antibodies. It is sometimes desirable toscreen for stable monomeric B chain molecules, in an ELISA format, forexample, using antibodies that bind monomeric, but not pentameric Bchains. Additionally, the ability of experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) antigens to elicit neutralizing antibodies in anappropriate animal model such as mouse or monkey can be screened. Forexample, antibodies that bind to the B chain and prevent its binding toits specific ganglioside receptors on the surface of intestinalepithelial cells may prevent disease. Similarly antibodies that bind tothe B chain and prevent its pentamerization or block A chain binding maybe useful in preventing disease.

The bacterial antigens that can be improved by stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly for use as vaccines also include, but are notlimited to, Helicobacter pylori antigens CagA and VacA (Blaser (1996)Aliment. Pharmacol. Ther. 1: 73-7; Blaser and Crabtree (1996) Am. JClin. Pathol. 106: 565-7; Censini et al. (1996) Proc. Nat'l. Acad. Sci.USA 93: 14648-14643).

Other suitable H. pylori antigens include, for example, fourimmunoreactive proteins of 45-65 kDa as reported by Chatha et al. (1997)Indian J Med. Res. 105: 170-175 and the H. pylori GroES homologue (HspA)(Kansau et al. (1996) Mol. Microbiol. 22: 1013-1023. Other suitablebacterial antigens include, but are not limited to, the 43-kDa and thefimbrilin (41 kDa) proteins of P. gingivalis (Boutsl et al. (1996) OralMicrobiol. Immunol. 11: 236-241); pneumococcal surface protein A (Brileset al. (1996) Ann. NY Acad. Sci. 797: 118-126); Chlamydia psittaciantigens, 80-90 kDa protein and 110 kDa protein (Buendia et al. (1997)FEMS Microbiol. Lett. 150: 113-9); the chlainydial exoglycolipid antigen(GLXA) (Whittum-Hudson et al. (1996) Nature Med. 2: 1116-1121);Chlamlydia pneumoniae species-specific antigens in the molecular weightranges 92-98, 51-55, 43-46 and 31.5-33 kDa and genus-specific antigensin the ranges 12, 26 and 65-70 kDa (Halme et al. (1997) Scand. JImmunol. 45: 378-84); Neisseria gonorrhoeae (GC) or Escherichia coliphase-variable opacity (Opa) proteins (Chen and Gotschlich (1996) Proc.Nat'l. Acad. Sci. USA 93: 14851-14856), any of the twelve immunodominantproteins of Schistosoma mansoni (ranging in molecular weight from 14 to208 kDa) as described by Cutts and Wilson (1997) Parasitology 114:245-55; the 17-kDa protein antigen of Brucella abortus (De Mot et al.(1996) Curr. Microbiol. 33: 26-30); a gene homolog of the 17-kDa proteinantigen of the Gram-negative pathogen Brucella abortus identified in thenocardioform actinomycete Rhodococcus sp. N186/21 (De Mot et al. (1996)Curr. Microbiol. 33: 26-30); the staphylococcal enterotoxins (SEs) (Woodet al. (1997) FEMS Immunol. Med. Microbiol. 17: 1-10), a 42-kDa M.hyopneumoniae NrdF ribonucleotide reductase R2 protein or 15-kDa subunitprotein of M. hyopneumoniae (Fagan et al. (1997) Infect. Immun. 65:2502-2507), the meningococcal antigen PorA protein (Feavers et al.(1997) Clin. Diagn. Lab. Immunol. 3: 444-50); pneumococcal surfaceprotein A (PspA) (McDaniel et al. (1997) Gene Ther. 4: 375-377); F.tularensis outer membrane protein FopA (Fulop et al. (1996) FEMSImmunol.Med. Microbiol. 13: 245-247); the major outer membrane protein withinstrains of the genus Actinobacillus (Hartmann et al. (1996) Zentralbl.Bakteriol. 284: 255-262); p60 or listeriolysin (Hly) antigen of Listeriamonocytogenes (Hess et al. (1996) Proc. Nat'l. Acad. Sci. USA 93:1458-1463); flagellar (G) antigens observed on Salmonella enteritidisand S. pullorum (Holt and Chaubal (1997) J. Clin. Microbiol. 35:1016-1020); Bacillus anthracis protective antigen (PA) (Ivins et al.(1995) Vaccine 13: 1779-1784); Echinococcus granulosus antigen 5 (Joneset al. (1996) Parasitology 113: 213-222); the rol genes of Shigelladvsenteriae I and Escherichia coli K-12 (Klee et al. (1997) J.Bacteriol. 179: 2421-2425); cell surface proteins Rib and alpha of groupB streptococcus (Larsson et al. (1996) Infect. Immun. 64: 3518-3523);the 37 kDa secreted polypeptide encoded on the 70 kb virulence plasmidof pathogenic Yersinia spp. (Leary et al. (1995) Contrib. Microbiol.Immunol. 13: 216-217 and Roggenkamp et al. (1997) Infect. Immun. 65:446-51); the OspA (outer surface protein A) of the Lyme diseasespirochete Borrelia burgdorferi (Li et al. (1997) Proc. Nat'l. Acad.Sci. USA 94: 3584-3589, Padilla et al. (1996) J Infect. Dis. 174:739-746, and Wallich et al. (1996) Infection 24: 396-397); the Brucellamelitensis group 3 antigen gene encoding Omp28 (Lindler et al. (1996)Infect. Immun. 64: 2490-2499); the PAc antigen of Streptococcus mutans(Murakami et al. (1997) Infect. Immun. 65: 794-797); pneumolysin,Pneumococcal neuraminidases, autolysin, hyaluronidase, and the 37 kDapneumococcal surface adhesin A (Paton et al. (1997) Microb. Drug Resist.3: 1-10); 29-32, 41-45, 63−71×10(3) MW antigens of Salmonella typhi(Perez et al. (1996) Immunology 89: 262-267); K-antigen as a marker ofKlebsiella pneumoniae (Priamukhina and Morozova (1996) Klin. Lab. Diagn.47-9); nocardial antigens of molecular mass approximately 60, 40, and15-10 kDa (Prokesova et al. (1996) Int. J Immunopharmacol. 18: 661-668);Staphylococcus aureus antigen ORF-2 (Rieneck et al. (1997) BiochimBiophys Acta 1350: 128-132); GlpQ antigen of Borrelia hermsii (Schwan etal. (1996) J Clin. Microbiol. 34: 2483-2492); cholera protective antigen(CPA) (Sciortino (1996) J. Diarrhoeal Dis. Res. 14: 16-26); a 190-kDaprotein antigen of Streptococcus mutans (Senpuku et al. (1996) OralMicrobiol. Immunol. 11: 121-128); Anthrax toxin protective antigen (PA)(Sharma et al. (1996) Protein Expr. Purif. 7: 33-38); Clostridiumperfringens antigens and toxoid (Strom et al. (1995) Br. J. Rheumatol.34: 1095-1096); the SEF14 fimbrial antigen of Salmonella enteritidis(Thorns et al. (1996) Microb. Pathog. 20: 235-246); the Yersinia pestiscapsular antigen (F I antigen) (Titball et al. (1997) Infect. Immun. 65:1926-1930); a 35-kilodalton protein of Mycobacterium leprae (Triccas etal. (1996) Infect. Immun. 64: 5171-5177); the major outer membraneprotein, CD, extracted from Moraxella (Branhamella) catarrhalis (Yang etal. (1997) FEMS Immunol. Med. Microbiol. 17: 187-199); pH6 antigen (PsaAprotein) of Yersinia pestis (Zav'yalov et al. (1996) FEMS Immunol. Med.Microbiol. 14: 53-57); a major surface glycoprotein, gp63, of Leishmaniamajor (Xu and Liew (1994) Vaccine 12: 1534-1536; Xu and Liew (1995)Immunology 84: 173-176); mycobacterial heat shock protein 65,mycobacterial antigen (Mycobacterium leprae hsp65) (Lowrie et al. (1994)Vaccine 12: 1537-1540; Ragno et al. (1997) Arthritis Rheum. 40: 277-283;Silva (1995) Braz. J Med. Biol. Res. 28: 843-851); Mycobacteriumtuberculosis antigen 85 (Ag85) (Huygen et al. (1996) Nat. Med. 2:893-898); the 45/47 kDa antigen complex (APA) of Mycobacteriumtuberculosis, M. bovis and BCG (Horn et al. (1996) J Immunol. Methods197: 151-159); the mycobacterial antigen, 65-kDa heat shock protein,hsp65 (Tascon et al. (1996) Nat. Med. 2: 888-892); the mycobacterialantigens MPB64, MPB70, MPB57 and alpha antigen (Yamada et al. (1995)Kekkaku 70: 639-644); the M. tuberculosis 3 8 kDa protein (Vordenneieret al. (1995) Vaccine 13: 1576-1582); the MPT63, MPT64 and MPT-59antigens from Mycobacterium tuberculosis (Manca et al. (1997) Infect.Immun. 65: 16-23; Oettinger et al. (1997) Scand. J Immunol. 45: 499-503;Wilcke et al. (1996) Tuber. Lung Dis. 77: 250-256); the 35-kilodaltonprotein of Mycobacterium leprae (Triccas et al. (1996) Infect. Immun.64: 5171-5177); the ESAT-6 antigen of virulent mycobacteria (Brandt etal. (1996) J Immunol. 157: 3527-3533; Pollock and Andersen (1997) JInfect. Dis. 175: 1251-1254); A˜vcobacterium tuberculosis 16-kDa antigen(Hsp16.3) (Chang et al. (1996) J Biol. Chem. 271: 7218-7223); and the18-kilodalton protein of Mycobacterium leprae (Baumgart et al. (1996)Infect. Immun. 64: 2274-2281).

2.9.1.2. Viral Pathogens

The methods of the invention are also useful for obtaining recombinantnucleic acids and polypeptides that have enhanced ability to induce animmune response against viral pathogens. While the bacterialrecombinants described above are typically administered in polypeptideform, recombinants that confer viral protection are preferablyadministered in nucleic acid form, as genetic vaccines.

One illustrative example is the Hantaan virus. Glycoproteins of thisvirus typically accumulate at the membranes of the Golgi apparatus ofinfected cells. This poor expression of the glycoprotein prevents thedevelopment of efficient genetic vaccines against these viruses. Themethods of the invention solve this problem by performing stochastic(e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly on nucleic acids that encodethe glycoproteins and identifying those recombinants that exhibitenhanced expression in a host cell, and/or for improved immunogenicitywhen administered as a genetic vaccine. A convenient screening methodfor these methods is to express the experimentally generatedpolynucleotides as fusion proteins to PIG, which results in display ofthe polypeptides on the surface of the host cell (Whitehorn et al.(1995) Biotechnology (N Y) 13:1215-9). Fluorescence-activated cellsorting is then used to sort and recover those cells that express anincreased amount of the antigenic polypeptide on the cell surface. Thispreliminary screen can be followed by immunogenicity tests in mammals,such as mice. Finally, in preferred embodiments, those recombinantnucleic acids are tested as genetic vaccines for their ability toprotect a test animal against challenge by the virus.

The flaviviruses are another example of a viral pathogen for which themethods of the invention are useful for obtaining a experimentallygenerated polypeptide or genetic vaccine that is effective against aviral pathogen. The flaviviruses consist of three clusters ofantigenically related viruses: Dengue 1-4 (62-77% identity), Japanese,St. Louis and Murray Valley encephalitis viruses (75-82% identity), andthe tick-borne encephalitis viruses (77-96% identity). Dengue virus caninduce protective antibodies against SLE and Yellow fever (40-50%identity), but few efficient vaccines are available. To obtain geneticvaccines and experimentally generated polypeptides that exhibit enhancedcross-reactivity and immunogenicity, the polynucleotides that encodeenvelope proteins of related viruses are subjected to stochastic (e.g.polynucleotide shuffling & interrupted synthesis) and non-stochasticpolynucleotide reassembly. The resulting experimentally generatedpolynucleotides can be tested, either as genetic vaccines or by usingthe expressed polypeptides, for ability to induce a broadly reactingneutralizing antibody response. Finally, those clones that are favorablein the preliminary screens can be tested for ability to protect a testanimal against viral challenge.

Viral antigens that can be evolved by stochastic (e.g. polynucleotideshuffling & interrupted synthesis) and non-stochastic polynucleotidereassembly for improved activity as vaccines include, but are notlimited to, influenza A virus N2 neuraminidase (Kilbourne et al. (1995)Vaccine 13: 1799-1803); Dengue virus envelope (E) and premembrane (prM)antigens (Feighny et al. (1994) Am. J Trop. Med. Hyg. 50: 322-328;Putnak et al. (1996) Am. J Trop. Med. Hyg. 5 5: 504-10); HIV antigensGag, Pol, Vif and Nef (Vogt et al. (1995) Vaccine 13: 202-208); HIVantigens gp120 and gp 160 (Achour et al. (1995) Cell. Mol. Biol. 41:395-400; Hone et al. (1994) Dev. Biol. Stand. 82: 159-162); gp41 epitopeof human immunodeficiency virus (Eckhart et al. (1996) J Gen. Virol. 77:2001-2008); rotavirus antigen VP4 (Mattion et al. (1995) J Virol. 69:5132-5137); the rotavirus protein VP7 or VP7sc (Emslie et al. (1995) JVirol. 69: 1747-1754; Xu et al. (1995) J Gen. Virol. 76: 1971-1980);herpes simplex virus (HSV) glycoproteins gB, gC, gD, gE, gG, gH, and gI(Fleck et al. (1994) Med. Microbiol. Immunol. (Berl) 183: 87-94[Mattion, 1995]; Ghiasi et al. (1995) Invest. Opthalmol. Vis. Sci. 36:1352-1360; McLean et al. (1994) J Infect. Dis. 170: 1100-1109);immediate-early protein ICP47 of herpes simplex virus-type 1 (HSV-1)(Banks et al. (1994) Virology 200: 236-245); immediate-early (IE)proteins ICP27, ICPO, and ICP4 of herpes simplex virus (Manickan et al.(1995) J Virol. 69: 4711-4716); influenza virus nucleoprotein andhemagglutinin (Deck et al. (1997) Vaccine 15: 71-78; Fu et al. (1997) JVirol. 71: 2715-2721); B 19 parvovirus capsid proteins VP1 (Kawase etal. (1995) Virology 211: 359-366) or VP2 (Brown et al. (1994) Virology198: 477-488); Hepatitis B virus core and e antigen (Schodel et al.(1996) Intervirology 39:104-106); hepatitis B surface antigen (Shiau andMurray (1997) J. Med. Virol. 51: 159-166); hepatitis B surface antigenfused to the core antigen of the virus (Id.); Hepatitis B viruscore-preS2 particles (Nemeckova et al. (1996) Acta Virol. 40: 273-279);HBV preS2-S protein (Kutinova et al. (1996) Vaccine 14: 1045-1052); VZVglycoprotein I (Kutinova et al. (1996) Vaccine 14: 1045-1052); rabiesvirus glycoproteins (Xiang et al. (1994) Virology 199: 132-140; Xuan etal. (1995) Virus Res. 36: 151-161) or ribonucleocapsid (Hooper et al.,(1994) Proc. Nat'l. Acad. Sci. USA 91: 10908-10912); humancytomegalovirus (HCMV) glycoprotein B (LTL55) (Britt et al. (1995) JInfect. Dis. 171: 18-25); the hepatitis C virus (HCV) nucleocapsidprotein in a secreted or a nonsecreted form, or as a fusion protein withthe middle (pre-S2 and S) or major (S) surface antigens of hepatitis Bvirus (HBV) (Inchauspe et al. (1997) DNA Cell Biol. 16: 185-195; Majoret al. (1995) J Virol. 69: 5798-5805); the hepatitis C virus antigens:the core protein (pC); E1 (pE1) and E2 (pE2) alone or as fusion proteins(Saito et al. (1997) Gastroenterology 112: 1321-1330); the gene encodingrespiratory syncytial virus fusion protein (PFP-2) (Falsey and Walsh(1996) Vaccine 14: 1214-1218; Piedra et al. (1996) Pediatr. Infect. Dis.J. 15: 23-31); the VP6 and VP7 genes of rotaviruses (Choi et al. (1997)Virology 232: 129-138; Jin et al. (1996) Arch. Virol. 141: 2057-2076);the E1, E2, E3, E4, E5, E6 and E7 proteins of human papillomavirus(Brown et al. (1994) Virology 201: 46-54; Dillner et al. (1995) CancerDetect. Prev. 19: 381-393; Krul et al. (1996) Cancer Immunol.Immunother. 43: 44-48; Nakagawa et al. (1997) J Infect. Dis. 175:927-931); a human T-lymphotropic virus type I gag protein (Porter et al.(1995) J Med. Virol. 45: 469-474); Epstein-Barr virus (EBV) gp340(Mackett et al. (1996) J Med. Virol. 50: 263-271); the Epstein-Barrvirus (EBV) latent membrane protein LMP2 (Lee et al. (1996) Eur. JImmunol. 26: 1875-1883); Epstein-Barr virus nuclear antigens 1 and 2(Chen and Cooper (1996) J Virol. 70: 4849-4853; Khanna et al. (1995)Virology 214: 633-637); the measles virus nucleoprotein (N) (Fooks etal. (1995) Virology 210: 456-465); and cytomegalovirus glycoprotein gB(Marshall et al. (1994) J Med. Virol. 43: 77-83) or glycoprotein gH(Rasmussen et al. (1994) J Infect. Dis. 170: 673-677).

2.9.2. Inflammatory and Autoimmune Diseases

Autoimmune diseases are characterized by immune response that attackstissues or cells of ones own body, or pathogen-specific immune responsesthat also are harmful for ones own tissues or cells, or non-specificimmune activation which is harmful for ones own tissues or cells.Examples of autoimmune diseases include, but are not limited to,rheumatoid arthritis, SLE, diabetes mellitus, myasthenia gravis,reactive arthritis, ankylosing spondylitis, and multiple sclerosis.These and other inflammatory conditions, including IBD, psoriasis,pancreatitis, and various immunodeficiencies, can be treated usinggenetic vaccines that include vectors and other components obtainedusing the methods of the invention (e.g. using antigens that areoptimized using the methods of the invention).

These conditions are often characterized by an accumulation ofinflammatory cells, such as lymphocytes, macrophages, and neutrophils,at the sites of inflammation. Altered cytokine production levels areoften observed, with increased levels of cytokine production. Severalautoimmune diseases, including diabetes and rheumatoid arthritis, arelinked to certain MHC haplotypes. Other autoimmune-type disorders, suchas reactive arthritis, have been shown to be triggered by bacteria suchas Yersinia and Shigella, and evidence suggests that several otherautoimmune diseases, such as diabetes, multiple sclerosis, rheumatoidarthritis, may also be initiated by viral or bacterial infections ingenetically susceptible individuals.

Current strategies of treatment generally include anti-inflammatorydrugs, such as NSAID or cyclosporin, and antiproliferative drugs, suchas methotrexate. These therapies are non-specific, so a need exists fortherapies having greater specificity, and for means to direct the immuneresponses towards the direction that inhibits the autoimmune process.

The present invention provides several strategies by which these needscan be fulfilled. First, the invention provides methods of obtainingvaccines which exhibit improved delivery of tolerogenic antigens (e.g.methods of obtaining antigens having greater tolerogenicity and/or haveimproved antigenicity), antigens which have improved antigenicity,genetic vaccine-mediated tolerance, and modulation of the immuneresponse by inclusion of appropriate accessory molecules. In a preferredembodiment, the vaccines (e.g. optimized antigens) prepared according tothe invention exhibit improved induction of tolerance by oral delivery.

Oral tolerance is characterized by induction of immunological toleranceafter oral administration of large quantities of antigen (Chen et al.(1995) Science 265: 1237-1240; Haq et al. (1995) Science 268: 714-716).In animal models, this approach has proven to be a very promisingapproach to treat autoimmune diseases, and clinical trials are inprogress to address the efficacy of this approach in the treatment ofhuman autoimmune diseases, such as rheumatoid arthritis and multiplesclerosis (Chen et al. (1994) Science 265:123 7-40; Whitacre et al.(1996) Clin. Immunol. Immunopathol. 80: S31-9; Hohol et al. (1996) Ann.N.Y. Acad Sci. 778:243-50). It has also been suggested that induction oforal tolerance against viruses used in gene therapy might reduce theimmunogenicity of gene therapy vectors.

However, the amounts of antigen required for induction of oral toleranceare very high and improved methods for oral delivery of antigenicproteins would significantly improve the efficacy of induction of oraltolerance.

Expression library immunization (Barry et al. (1995) Nature 3 77: 632)is a particularly useful method of screening for optimal antigens foruse in genetic vaccines. For example, to identify autoantigens presentin Yersinia, Shigella, and the like, one can screen for induction of Tcell responses in HLA-B27 positive individuals. Complexes that includeepitopes of bacterial antigens and MHC molecules associated withautoimmune diseases, e.g., HLA-B27 in association with Yersinia antigenscan be used in the prevention of reactive arthritis and ankylosingspondylitis in HLA-B27 positive individuals.

Treatment of autoimmune and inflammatory conditions can involve not onlyadministration of tolerogenic antigens, but also the use of acombination of cytokines, costimulatory molecules, and the like. Suchcocktails are formulated for induction of a favorable immune response,typically induction of autoantigen-specific tolerance. Cocktails canalso include, for example, CD1, which is crucially involved inrecognition of self antigens by a subset of T cells (Porcelli (1995)Adv. Immunol. 5 9: 1). Genetic vaccine vectors and cocktails that skewimmune responses towards the T_(H)2 are often used in treatingautoimmune and inflammatory conditions, both with antigen-specific andantigen non-specific vectors.

Screening of genetic vaccines and accessory molecules (e.g. andoptimized antigens) can be done in animal models which are known tothose of skill in the art. Examples of suitable models for variousconditions include collagen induced arthritis, the NFS/sld mouse modelof human Sjogren's syndrome; a 120 kD organ-specific autoantigenrecently identified as an analog of human cytoskeletal protein α-fodrin(Haneji et al. (1997) Science 276: 604), the New Zealand Black/White F1hybrid mouse model of human SLE, NOD mice, a mouse model of humandiabetes mellitus, fas/fas ligand mutant mice, which spontaneouslydevelop autoimmune and lymphoproliferative disorders (Watanabe-Fukunagaet al. (1992) Nature 356: 314), and experimental autoimmuneencephalomyelitis (EAE), in which myelin basic protein induces a diseasethat resembles human multiple sclerosis.

Autoantigens (that can be experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis) according tothe methods of the invention) that are useful in genetic vaccines fortreating multiple sclerosis include, but are not limited to, myelinbasic protein (Stinissen et al. (1996) J Neurosci. Res. 45: 500-511) ora fusion protein of myelin basic protein and proteolipid protein inmultiple sclerosis (Elliott et al. (1996) J Clin. Invest. 98:1602-1612), proteolipid protein (PLP) (Rosener et al. (1997) JNeuroimmunol. 75: 28-34), 2′,3′-cyclic nucleotide 3′-phosphodiesterase(CNPase) (Rosener et al. (1997) J Neuroimmunol. 75: 28-34), the EpsteinBarr virus nuclear antigen-1 (EBNA-1) in multiple sclerosis (Vaughan etal. (1996) J Neuroimmunol. 69: 95-102), HSP70 in multiple sclerosis(Salvetti et al. (1996) J Neuroimmunol. 65: 143-53; Feldmann et al.(1996) Cell 85: 307).

Target antigens that, after reassembly (optionally in combination withother directed evolution methods described herein) according to themethods of the invention, can be used to treat scleroderma, systemicsclerosis, and systemic lupus erythematosus include, for example,(-2-GPI, 50 kDa glycoprotein (Blank et al. (1994) J Autoimmun. 7:441-455), Ku (p70/p80) autoantigen, or its 80-kd subunit protein (Honget al. (1994) Invest. Opthalmol. Vis. Sei. 35: 4023-4030; Wang et al.(1994) J Cell Sci. 107: 3223-3233), the nuclear autoantigens La (SS-B)and Ro (SS-A) (Huang et al. (1997) J Clin. Immunol. 17: 212-219;Igarashi et al. (1995) Autoimmunity 22: 33-42; Keech et al. (1996) Clin.Exp. Immunol. 104: 255-263; Manoussakis et al. (1995) J Autoimmun. 8:959-969; Topfer et al. (1995) Proc. Nat'l. Acad. Sci. USA 92: 875-879),proteasome (-type subunit C9 (Feist et al. (1996) J Exp. Med. 184:1313-1318), Scleroderma antigens Rpp 30, Rpp 38 or Scl-70 (Eder et al.(1997) Proc. Nat'l. Acad. Sci. USA 94: 1101-1106; Hietarinta et al.(1994) Br. J Rheumatol. 33: 323-326), the centrosome autoantigen PCM-1(Bao et al. (1995) Autoimmunity 22: 219-228), polymyositis-sclerodermaautoantigen (PM-Scl) (Kho et al. (1997) J Biol. Chem. 272: 13426-13431),scleroderma (and other systemic autoimmune disease) autoantigen CENP-A(Muro et al. (1996) Clin. Immunol. Immunopathol. 78: 86-89), U5, a smallnuclear ribonucleoprotein (snRNP) (Okano et al. (1996) Clin. Immunol.Immunopathol. 81: 41-47), the 100-kd protein of PM-Scl autoantigen (Geet al. (1996) Arthritis Rheum. 39: 1588-1595), the nucleolar U3- andTh(7-2) ribonucleoproteins (Verheijen et al. (1994) J. Immunol. Methods169: 173-182), the ribosomal protein L7 (Neu et al. (1995) Clin. Exp.Immunol. 100: 198-204), hPop 1 (Lygerou et al. (1996) EMBO J 15:5936-5948), and a 36-kd protein from nuclear matrix antigen (Deng et al.(1996) Arthritis Rheum. 39: 1300-1307).

Hepatic autoimmune disorders can also be treated using improvedrecombinant antigens that are prepared according to the methodsdescribed herein. Among the antigens that are useful in such treatmentsare the cytochromes P450 and UDP-glucuronosyl-transferases(Obermayer-Straub and Manns (1996) Baillieres Clin. Gastroenterol. 10:501-532), the cytochromes P450 2C9 and P450 1A2 (Bourdi et al. (1996)Chem. Res. Toxicol. 9: 1159-1166; Clemente et al. (1997) J Clin.Endocrinol. Metab. 82: 1353-1361), LC-1 antigen (Klein et al. (1996) JPediatr. Gastroenterol. Nutr. 23: 461-465), and a 230-kDaGolgi-associated protein (Funaki et al. (1996) Cell Struct. Funct. 21:63-72).

For treatment of autoimmune disorders of the skin, useful antigensinclude, but are not limited to, the 450 kD human epidermal autoantigen(Fujiwara et al. (1996) J Invest. Dermatol. 106: 1125-1130), the 230 kDand 180 kD bullous pemphigoid antigens (Hashimoto (1995) Keio J Med. 44:115-123; Murakami et al. (1996) J Dermatol. Sci. 13: 112-117), pemphigusfoliaceus antigen (desmoglein 1), pemphigus vulgaris antigen (desmoglein3), BPAg2, BPAg1, and type VII collagen (Batteux et al. (1997) J Clin.Immunol. 17: 228-233; Hashimoto et al. (1996) J Dermatol. Sci. 12:10-17), a 168-kDa mucosal antigen in a subset of patients withcicatricial pemphigoid (Ghohestani et al. (1996) J Invest. Dermatol.107: 136-139), and a 218-kd nuclear protein (218-kd Mi-2) (Seelig et al.(1995) Arthritis Rheum. 38: 1389-1399).

The methods of the invention are also useful for obtaining improvedantigens for treating insulin dependent diabetes mellitus, using one ormore of antigens which include, but are not limited to, insulin,proinsulin, GAD65 and GAD67, heat-shock protein 65 (hsp65), andislet-cell antigen 69 (ICA69) (French et al. (1997) Diabetes 46: 34-39;Roep (1996) Diabetes 45: 1147-1156; Schloot et al. (1997) Diabetologia40: 332-338), viral proteins homologous to GAD65 (Jones and Crosby(1996) Diabetologia 39: 1318-1324), islet cell antigen-relatedprotein-tyrosine phosphatase (PTP) (Cui et al. (1996) J Biol. Chem. 271:24817-24823), GM2-1 ganglioside (Cavallo et al. (1996) J Endocrinol.150: 113-120; Dotta et al. (1996) Diabetes 45: 1193-1196), glutarnicacid decarboxylase (GAD) (Nepom (1995) Curr. Opin. Immunol. 7: 825-830;Panina-Bordignon et al. (1995) J Exp. Med. 181: 1923-1927), an isletcell antigen (ICA69) (Karges et al. (1997) Biochim. Biophys. Acta 1360:97-101; Roep et al. (1996) Eur. J Immunol. 26: 1285-1289), Tep69, thesingle T cell epitope recognized by T cells from diabetes patients(Karges et al. (1997) Biochim. Biopkys. Acta 1360: 97-101), ICA 512, anautoantigen of type I diabetes (Solimena et al. (1996) EMBOJ. 15:2102-2114), an islet-cell protein tyrosine phosphatase and the 37-kDaautoantigen derived from it in type I diabetes (including IA-2, IA-2)(La Gasse et al. (1997) Mol. Med. 3: 163-173), the 64 kDa protein fromIn-111 cells or human thyroid follicular cells that isimmunoprecipitated with sera from patients with islet cell surfaceantibodies (ICSA) (Igawa et al. (1996) Endocr. J. 43: 299-306), phogrin,a homologue of the human transmembrane protein tyrosine phosphatase, anautoantigen of type I diabetes (Kawasaki et al. (1996) Biochem. Biophys.Res. Commun. 227: 440-447), the 40 kDa and 37 kDa tryptic fragments andtheir precursors IA-2 and IA-2 in IDDM (Lampasona et al. (1996) JImmunol. 157: 2707-2711; Notkins et al. (1996) J Autoimmun. 9: 677-682),insulin or a cholera toxoid-insulin conjugate (Bergerot et al. (1997)Proc. Nat'l. Acad. Sci. USA 94: 4610-4614), carboxypeptidase H, thehuman homologue of gp330, which is a renal epithelial glycoproteininvolved in inducing Heymann nephritis in rats, and the 38-kD isletmitochondrial autoantigen (Arden et al. (1996) J Clin. Invest. 97:551-561.

Rheumatoid arthritis is another condition that is treatable usingoptimized antigens prepared according to the present invention. Usefulantigens for rheumatoid arthritis treatment include, but are not limitedto, the 45 kDa DEK nuclear antigen, in particular onset juvenilerheumatoid arthritis and iridocyclitis (Murray et al. (1997) JRheumatol. 24: 560-567), human cartilage glycoprotein-39, an autoantigenin rheumatoid arthritis (Verheijden et al. (1997) Arthritis Rheum. 40:1115-1125), a 68 k autoantigen in rheumatoid arthritis (Blass et al.(1997) Ann. Rheum. Dis. 56: 317-322), collagen (Rosloniec et al. (1995)J Immunol. 155: 450-44511), collagen type II (Cook et al. (1996)Arthritis Rheum. 39: 1720-1727; Trentham (1996) Ann. N.Y. Acad. Sci.778: 306-314), cartilage link protein (Guerassimov et al. (1997) JRheumatol. 24: 959-964), ezrin, radixin and moesin, which areauto-immune antigens in rheumatoid arthritis (Wagatsuma et al. (1996)Mol. Immunol. 33: 1171-1176), and mycobacterial heat shock protein 65(Ragno et al. (1997) Arthritis Rheum. 40: 277-283).

Also among the conditions for which one can obtain an improved antigensuitable for treatment are autoimmune thyroid disorders. Antigens thatare useful for these applications include, for example, thyroidperoxidase and the thyroid stimulating hormone receptor (Tandon andWeetman (1994) J R. Coll. Physicians Lond. 28: 10-18), thyroidperoxidase from human Graves' thyroid tissue (Gardas et al. (1997)Biochem. Biophys. Res. Commun. 234: 366-370; Zimmer et al. (1997)Histochem. Cell. Biol. 107: 115-120), a 64-kDa antigen associated withthyroid-associated opthalmopathy (Zhang et al. (1996) Clin. Immunol.Immunopathol. 80: 236-244), the human TSH receptor (Nicholson et al.(1996) J Mol. Endocrinol. 16: 159-170), and the 64 kDa protein fromIn-111 cells or human thyroid follicular cells that isimmunoprecipitated with sera from patients with islet cell surfaceantibodies (ICSA) (Igawa et al. (1996) Endocr. J. 43: 299-306).

Other conditions and associated antigens include, but are not limitedto, Sjogren's syndrome (-fodrin; Haneji et al. (1997) Science 276:604-607), myastenia gravis (the human M2 acetylcholine receptor orfragments thereof, specifically the second extracellular loop of thehuman M2 acetylcholine receptor; Fu et al. (1996) Clin. Immunol.Immunopathol. 78: 203-207), vitiligo (tyrosinase; Fishman et al. (1997)Cancer 79: 1461-1464), a 450 kD human epidermal autoantigen recognizedby serum from individual with blistering skin disease, and ulcerativecolitis (chromosomal proteins HMG1 and HMG2; Sobajima et al. (1997)Clin. Exp. Immunol. 107: 135-140).

2.9.3. Allergy and Asthma

The invention also provides methods of obtaining reagents that areuseful for treating allergy. In one embodiment, the methods involvemaking a library of experimentally generated polynucleotides that encodean allergen, and screening the library to identify those experimentallygenerated polynucleotides that exhibit improved properties when used asimmunotherapeutic reagents for treating allergy. For example, specificimmunotherapy of allergy using natural antigens carries a risk ofinducing anaphylaxis, which can be initiated by cross-linking ofhigh-affinity Ig receptors on mast cells. Therefore, allergens that arenot recognized by pre-existing IgE are desirable. The methods of theinvention provide methods by which one can obtain such allergenvariants. Another improved property of interest is induction of broaderimmune responses, increased safety and efficacy.

Genetic vaccine vectors and other reagents obtained using the methods ofthe invention can be used to treat allergies and asthma. Allergic immuneresponses are results of complex interactions between B cells, T cells,professional antigen-presenting cells (APC), eosinophils and mast cells.These cells take part in allergic immune responses both as modulators ofthe immune responses and are also involved in producing factors directlyinvolved in initiation and maintenance of allergic responses.

Synthesis of Polyclonal and Allergen-Specific IgE Requires MultipleInteractions Between B Cells, T Cells and ProfessionalAntigen-Presenting Cells (APC).

Activation of naive, unprimed B cells is initiated when specific B cellsrecognize the allergen by cell surface immunoglobulin (sIg). However,costimulatory molecules expressed by activated T cells in both solubleand membrane-bound forms are necessary for differentiation of B cellsinto IgE-secreting plasma cells. Activation of T helper cells requiresrecognition of an antigenic peptide in the context of MHC class IImolecules on the plasma membrane of APC, such as monocytes, dendriticcells, Langerhans cells or primed B cells. Professional APC canefficiently capture the antigen and the peptide-MHC class II complexesare formed in a post-Golgi, proteolytic intracellular compartment andsubsequently exported to the plasma membrane, where they are recognizedby T cell receptor (TCR) (Monaco (1995) J Leuk. Biol. 57: 543-547). Inaddition, activated B cells express CD80 (B7-1) and CD86 (B7-2, B70),which are the counter receptors for CD28 and which provide acostimulatory signal for T cell activation resulting in T cellproliferation and cytokine synthesis (Bluestone (1995) Immunity 2:555-559). Since allergen-specific T cells from atopic individualsgenerally belong to the T_(H)2 cell subset, activation of these cellsalso leads to production of IL-4 and IL-13, which, together withmembrane-bound costimulatory molecules expressed by activated T helpercells, direct B cell differentiation into IgE-secreting plasma cells (deVries and Punnonen, In Cytokine Regulation of Humoral Immunity: Basicand Clinical Aspects, Ed. C M Snapper, John Wiley & Sons Ltd, WestSussex, UK, p. 195-215, 1996).

Mast cells and eosinophils are key cells in inducing allergic symptomsin target organs. Recognition of specific antigen by IgE bound tohigh-affinity IgE receptors on mast cells, basophils or eosinophilsresults in crosslinking of the receptors leading to degranulation of thecells and rapid release of mediator molecules, such as histamine,prostaglandins and leukotrienes, causing allergic symptoms.

Immunotherapy of allergic diseases currently includeshyposensibilization treatments using increasing doses of allergeninjected to the patient. These treatments result in skewing of immuneresponses towards T_(H)1 phenotype and increase the ratio of IgG/IgEantibodies specific for allergens. Because these patients havecirculating IgE antibodies specific for the allergens, these treatmentsinclude significant risk of anaphylactic reactions.

In these reactions, free circulating allergen is recognized by IgEmolecules bound to high-affinity IgE receptors on mast cells andeosinophils. Recognition of the allergen results in crosslinking of thereceptors leading to release of mediators, such as histamine,prostaglandins, and leukotrienes, which cause the allergic symptoms, andoccasionally anaphylactic reactions. Other problems associated withhyposensibilization include low efficacy and difficulties in producingallergen extracts reproducibly.

Genetic vaccines provide a means of circumventing the problems that havelimited the usefulness of previously known hyposensibilizationtreatments. For example, by expressing antigens on the surface of cells,such as muscle cells, the risk of anaphylactic reactions issignificantly reduced. This can be achieved by using genetic vaccinevectors that encode transmembrane forms of allergens. The allergens canalso be modified in such a way that they are efficiently expressed intransmembrane forms, further reducing the risk of anaphylacticreactions. Another advantage provided by the use of genetic vaccines forhyposensibilization is that the genetic vaccines can include cytokinesand accessory molecules which further direct the immune responsestowards the T_(H)1 phenotype, thus reducing the amount of IgE antibodiesproduced and increasing the efficacy of the treatments. Vectors can alsobe evolved to induce primarily IgG and IgM responses, with little or noIgE response.

Furthermore, stochastic (e.g. polynucleotide shuffling & interruptedsynthesis) and non-stochastic polynucleotide reassembly can be used togenerate allergens that are not recognized by the specific IgEantibodies preexisting in vivo, yet are capable of inducing efficientactivation of allergen-specific T cells. For example, using phagedisplay selection, one can express experimentally evolved (e.g. bypolynucleotide reassembly &/or polynucleotide site-saturationmutagenesis) allergens on phage, and only those that are not recognizedby specific IgE antibodies are selected. These are further screened fortheir capacity to induce activation of specific T cells. An efficient Tcell response is an indication that the T cell epitopes are functionallyintact, although the B cell epitopes were altered, as indicated by lackof binding of specific antibodies.

In these methods, polynucleotides encoding known allergens, or homologsor fragments thereof (e.g., immunogenic peptides) are inserted into DNAvaccine vectors and used to immunize allergic and asthmatic individuals.Alternatively, the experimentally evolved (e.g. by polynucleotidereassembly &/or polynucleotide site-saturation mutagenesis) allergensare expressed in manufacturing cells, such as E. coli or yeast cells,and subsequently purified and used to treat the patients or preventallergic disease. Stochastic (e.g. polynucleotide shuffling &interrupted synthesis) and non-stochastic polynucleotide reassembly canbe used to obtain antigens that activate T cells but cannot induceanaphylactic reactions. For example, a library of experimentallygenerated polynucleotides that encode allergen variants can be expressedin cells, such as antigen presenting cells, which are than contactedwith PBMC or T cell clones from atopic patients. Those library membersthat efficiently activate T_(H) cells from the atopic patients can beidentified by assaying for T cell proliferation, or by cytokinesynthesis (e.g., synthesis of IL-2, IL-4, IFN-γ. Those recombinantallergen variants that are positive in the in vitro tests can then besubjected to in vivo testing.

Examples of Allergies that can be Treated Include, but are not Limitedto, Allergies Against house dust mite, grass pollen, birch pollen,ragweed pollen, hazel pollen, Cockroach, Rice, Olive Tree Pollen, Fungi,Mustard, Bee Venom.

Antigens of interest include those of animals, including the mite (e.g.,Dermatophagoides pteronyssinus, Dermatophagoides farinae, Blomiatropicalis), such as the allergens der p1 (Scobie et al. (1994) Biochem.Soc. Trans. 22: 448S; Yssel et al. (1992) J Immunol. 148: 738-745), derp2 (Chua et al. (1996) Clin. Exp. Allergy 26: 829-837), der p3 (Smithand Thomas (1996) Clin. Exp. Allergy 26: 571-579), der p5, der p V (Linet al. (1994) J Allergy Clin. Immunol. 94: 989-996), der p6 (Bennett andThomas (1996) Clin. Exp. Allergy 26: 1150-1154), der p7 (Shen et al.(1995) Clin. Exp. Allergy 25: 416-422), der f2 (Yuuki et al. (1997) Int.Arch. Allergy Immunol. 112: 4448), der f3 (Nishiyarna et al. (1995) FEBSLett. 377: 62-66), der f7 (Shen et al. (1995) Clin. Exp. Allergy 25:1000-1006); Mag 3 (Fujikawa et al. (1996) Mol. Immunol. 33: 311-319).Also of interest as antigens are the house dust mite allergens Tyr p2(Eriksson et al. (1998) Eur. J Biochem. 251: 443-447), Lep d 1 (Schmidtet al. (1995) FEBS Lett. 3 70: 11-14), and glutathione S-transferase(O'Neill et al. (1995) Immunol Lett. 48: 103-107); the 25,589 Da, 219amino acid polypeptide with homology with glutathione S-transferases(ONeill et al. (1994) Biochim. Biophys. Acta. 1219: 521-528); Blo t 5(Arruda et al. (1995) Int. Arch. Allergy Immunol. 107: 456-457); beevenom phospholipase A2 (Carballido et al. (1994) J Allergy Clin.Immunol. 93: 758-767; Jutel et al. (1995) J Immunol. 154: 4187-4194);bovine dermal/dander antigens BDA 11 (Rautiainen et al. (1995) J.Invest. Dermatol. 105: 660-663) and BDA20 (Mantyj arvi et al. (1996) JAllergy Clin. Immunol. 97: 1297-1303); the major horse allergen Equ c1(Gregoire et al. (1996) J Biol. Chem. 271: 32951-32959); Jumper ant M.pilosula allergen Myr p 1 and its homologous allergenic polypeptides Myrp2 (Donovan et al. (1996) Biochem. Mol. Biol. Int. 39: 877-885); 1-13,14, 16 kD allergens of the mite Blomia tropicalis (Caraballo et al.(1996) J Allergy Clin. Immunol. 98: 573-579); the cockroach allergensBla g Bd90K (Helm et al. (1996) J Allergy Clin. Immunol. 98: 172-80) andBla g 2 (Arruda et al. (1995) J Biol. Chem. 270: 19563-19568); thecockroach Cr-PI allergens (Wu et al. (1996) J Biol. Chem. 271:17937-17943); fire ant venom allergen, Sol i 2 (Schmidt et al. (1996) JAllergy Clin. Immunol. 98: 82-88); the insect Chironomus thumini majorallergen Chi t 1-9 (Kipp et al. (1996) Int. Arch. Allergy Immunol. 110:348-353); dog allergen Can f 1 or cat allergen Fel d 1 (Ingram et al.(1995) J Allergy Clin. Immunol. 96: 449-456); albumin, derived, forexample, from horse, dog or cat (Goubran Botros et al. (1996) Immunology88: 340-347); deer allergens with the molecular mass of 22 kD, 25 kD or60 kD (Spitzauer et al. (1997) Clin. Exp. Allergy 27: 196-200); and thekd major allergen of cow (Ylonen et al. (1994) J Allergy Clin. Immunol.93: 851-858).

Pollen and grass allergens are also useful in vaccines, particularlyafter optimization of the antigen by the methods of the invention. Suchallergens include, for example, Hor v9 (Astwood and Hill (1996) Gene182: 53-62, Lig v 1 (Batanero et al. (1996) Clin. Exp. Allergy 26:1401-1410); Lol p 1 (Muller et al. (1996) Int. Arch. Allergy Immunol.109: 352-355), Lol p II (Tamborini et al. (1995) Mol. Immunol. 32:505-513), Lol pVA, Lol pVB (Ong et al. (1995) Mol. Immunol. 32:295-302), Lol p 9 (Blaher et al. (1996) J Allergy Clin. Immunol. 98:124-132); Par J I (Costa et al. (1994) FEBS Lett. 341: 182-186; Sallustoet al. (1996) J Allergy Clin. Immunol. 97: 627-637), Parj 2.0101 (Duroet al. (1996) FEBS Lett. 399: 295-298); Bet vl (Faber et al. (1996) JBiol. Chem. 271: 19243-19250), Bet v2 (Rihs et al. (1994) Int. Arch.Allergy Immunol. 105: 190-194); Dac g3 (Guerin-Marchand et al. (1996)Mol. Immunol. 33: 797-806); Phl p 1 (Petersen et al. (1995) J AllergyClin. Immunol. 95: 987-994), Phl p 5 (Muller et al. (1996) Int. Arch.Allergy Immunol. 109: 352-355), Phl p 6 (Petersen et al. (1995) Int.Arch. Allergy Immunol. 108: 55-59); Cry j I (Sone et al. (1994) Biochem.Biophys. Res. Commun. 199: 619-625), Cry j Il (Namba et al. (1994) FEBSLett. 353: 124-128); Cor a 1 (Schenk et al. (1994) Eur. J Biochem. 224:717-722); cyn d 1 (Smith et al. (1996) J Allergy Clin. Immunol. 98:331-343), cyn d 7 (Suphioglu et al. (1997) FEBS Lett. 402: 167-172); Phaa 1 and isoforms of Pha a 5 (Suphioglu and Singh (1995) Clin. Exp.Allergy 25: 853-865); Cha o 1 (Suzuki et al. (1996) Mol. Immunol. 33:451-460); profilin derived, e.g, from timothy grass or birch pollen(Valenta et al. (1994) Biochem. Biopkys. Res. Commun. 199:106-118);P0149 (Wu et al. (1996) Plant Mol. Biol. 32: 1037-1042); Ory s1 (Xu etal. (1995) Gene 164:255-259); and Amb a V and Amb t5 (Kim et al. (1996)Mol. Immunol. 33: 873-880; Zhu et al. (1995) J Immunol. 155: 5064-5073).

Vaccines against food allergens can also be developed using the methodsof the invention. Suitable antigens for reassembly (optionally incombination with other directed evolution methods described herein)include, for example, profilin (Rihs et al. (1994) Int. Arch. AllergyImmunol. 105: 190-194); rice allergenic cDNAs belonging to thealpha-amylase/trypsin inhibitor gene family (Alvarez et al. (1995)Biochim Biophys Acta 1251: 201-204); the main olive allergen, Ole e I(Lombardero et al. (1994) Clin Exp Allergy 24: 765-770); Sin a 1, themajor allergen from mustard (Gonzalez De La Pena et al. (1996) Eur JBiochem. 237: 827-832); parvalbumin, the major allergen of salmon(Lindstrom et al. (1996) Scand. J Immunol. 44: 335-344); appleallergens, such as the major allergen Mal d 1 (Vanek-Krebitz et al.(1995) Biochem. Biophys. Res. Commun. 214: 538-551); and peanutallergens, such asAra h I (Burks et al. (1995) J Clin. Invest. 96:1715-1721).

The methods of the invention can also be used to develop recombinantantigens that are effective against allergies to fungi. Fungal allergensuseful in these vaccines include, but are not limited to, the allergen,Cla h III, of Cladosporium herbarum (Zhang et al. (1995) J Immunol. 154:710-717); the allergen Psi c 2, a fungal cyclophilin, from thebasidiomycete Psilocybe cubensis (Horner et al. (1995) Int. Arch.Allergy Immunol. 107: 298-300); hsp 70 cloned from a cDNA library ofCladosporium herbarum (Zhang et al. (1996) Clin Exp Allergy 26: 88-95);the 68 kD allergen of Penicillium notatum (Shen et al. (1995) Clin. Exp.Allergy 26: 350-356); aldehyde dehydrogenase (ALDH) (Achatz et al.(1995) Mol. Immunol. 32: 213-227); enolase (Achatz et al. (1995) Mol.Immunol. 32: 213-227); YCP4 (Id.); acidic ribosomal protein P2 (Id.).

Other allergens that can be used in the methods of the invention includelatex allergens, such as a major allergen (Hev b 5) from natural rubberlatex (Akasawa et al. (1996) J Biol. Chem. 271: 25389-25393; Slater etal. (1996) J Biol. Chem. 271: 25394-25399).

The invention also provides a solution to another shortcoming of geneticvaccination as a treatment for allergy and asthma. While geneticvaccination primarily induces CD8⁺ T cell responses, induction ofallergen-specific IgE responses is dependent on CD4⁺ T cells and theirhelp to B cells. T_(H)2-type cells are particularly efficient ininducing IgE synthesis because they secrete high levels of IL-4, IL-5and IL-13, which direct Ig isotype switching to IgE synthesis. IL-5 alsoinduces eosinophilia. The methods of the invention can be used todevelop genetic vaccines that efficiently induce CD4⁺ T cell responses,and direct differentiation of these cells towards the T_(H)1 phenotype.

The invention also provides methods by which the level of antigenrelease by a genetic vaccine vector is regulated. Regulation of theantigen dose is crucial at the onset of hyposensibilization for safetyreasons. Low antigen levels are preferably used at first, with theantigen level increasing once evidence has been obtained that theantigen does not induce adverse effects in the individual. Thestochastic (e.g. polynucleotide shuffling & interrupted synthesis) andnon-stochastic polynucleotide reassembly methods of the invention allowgeneration of genetic vaccine vectors that induce expression ofdifferent (high and low) levels of antigen. For example, two or moredifferent evolved promoters can be used for antigen expression.Alternatively, the antigen gene itself can be evolved for differentlevels of expression by, for example, altering codon usage. Vectors thatinduce different levels of antigen expression can be screened by use ofspecific monoclonal antibodies, and cell sorting (e.g, FACS).

2.9.4. Cancer

Immunotherapy has great promise for the treatment of cancer andprevention of metastasis. By inducing an immune response againstcancerous cells, the body's immune system can be enlisted to reduce oreliminate cancer. (e.g. using the improved antigens obtained using themethods of the invention). Genetic vaccines prepared using the methodsof the invention, as well as accessory molecules described herein,provide cancer immunotherapies of increased effectiveness compared tothose that are presently available.

One approach to cancer immunotherapy is vaccination using geneticvaccines that include or encode antigens that are specific for tumorcells or by injecting the patients with purified recombinant cancerantigens. The methods of the invention can be used for (obtainingantigens that exhibit an) enhancement of immune responses against knowntumor-specific antigens, and also to search for novel protectiveantigenic sequences. Genetic vaccines that exhibit optimized antigenexpression, processing, and presentation can be obtained as describedherein. The methods of the invention are also suitable for obtainingoptimized cytokines, costimulatory molecules, and other accessorymolecules that are effective in induction of an antitumor immuneresponse, as well as for obtaining genetic vaccines and cocktails thatinclude these and other components present in optimal combinations. Theapproach used for each particular cancer can vary. For treatment ofhormone-sensitive cancers (for example, breast cancer and prostatecancer), methods of the invention can be used to obtain optimizedhormone antagonists. For highly immunogenic tumors, including melanoma,one can screen for genetic vaccine vectors (recombinant antigens) thatoptimally boost the immune response against the tumor.

Breast Cancer, in Contrast, is of Relatively Low Immunogenicity andExhibits Slow Progression, so Individual Treatments can be Designed forEach Patient. Prevention of Metastasis is Also a Goal in Design ofGenetic Vaccines.

Among the tumor-specific antigens that can be used in the antigenreassembly (optionally in combination with other directed evolutionmethods described herein) methods of the invention are: bullouspemphigoid antigen 2, prostate mucin antigen (PMA) (Beckett and Wright(1995) Int. J Cancer 62: 703-710), tumor associated Thomsen-Friedenreichantigen (Dahlenborg et al. (1997) Int. J Cancer 70: 63-71),prostate-specific antigen (PSA) (Dannull and Belldegrun (1997) Br. JUrol. 1: 97-103), luminal epithelial antigen (LEA. 135) of breastcarcinoma and bladder transitional cell carcinoma (TCC) (Jones et al.(1997) Anticancer Res. 17: 685-687), cancer-associated serum antigen(CASA) and cancer antigen 125 (CA 125) (Kierkegaard et al. (1995)Gynecol. Oncol. 59: 251-254), the epithelial glycoprotein 40 (EGP40)(Kievit et al. (1997) Int. J Cancer 71: 237-245), squamous cellcarcinoma antigen (SCC) (Lozza et al. (1997) Anticancer Res. 17:525-529), cathepsin E (Mota et al. (1997) Ant. J Pathol. 150:1223-1229), tyrosinase in melanoma (Fishman et al. (1997) Cancer 79:1461-1464), cell nuclear antigen (PCNA) of cerebral cavemomas (Noteletet al. (1997) Surg. Neurol. 47: 364-370), DF3/MUCl breast cancer antigen(Apostolopoulos et al. (1996) Immunol. Cell. Biol. 74: 457-464; Pandeyet al. (1995) Cancer Res. 5 5: 4000-4003), carcinoembryonic antigen(Paone et al. (1996) J Cancer Res. Clin. Oncol. 122: 499-503; Schlom etal. (1996) Breast Cancer Res. Treat. 38: 27-39), tumor-associatedantigen CA 19-9 (Tolliver and O'Brien (1997) South Med. J. 90: 89-90;Tsuruta et al. (1997) Urol. Int. 5 8: 20-24), human melanoma antigensMART-I/Melan-A27- and gplOO (Kawakami and Rosenberg (1997) Int. Rev.Immunol. 14: 173-192; Zajac et al. (1997) Int. J Cancer 71: 491-496),the T and Tn pancarcinoma (CA) glycopeptide epitopes (Springer (1995)Crit. Rev. Oncog. 6: 57-85), a 35 kD tumor-associated autoantigen inpapillary thyroid carcinoma (Lucas et al. (1996) Anticancer Res. 16:2493-2496), KH-I adenocarcinoma antigen (Deshpande and Danishefsky(1997) Nature 387: 164-166), the A60 mycobacterial antigen (Maes et al.(1996) J Cancer Res. Clin. Oncol. 122: 296-300), heat shock proteins(HSPs) (Blachere and Srivastava (1995) Semin. Cancer Biol. 6: 349-355),and MAGE, tyrosinase, melan-A and gp75 and mutant oncogene products(e.g., p53, ras, and HER-2/neu (Bueler and Mulligan (1996) Mol. Med. 2:545-555; Lewis and Houghton (1995) Semin. Cancer Biol. 6: 321-327;Theobald et al. (1995) Proc. Nat'l. Acad. Sci. USA92: 11993-11997).

2.9.5. Parasites

Antigens from parasites can also be optimized by the methods of theinvention. These include, but are not limited to, the schistosomegut-associated antigens CAA (circulating anodic antigen) and CCA(circulating cathodic antigen) in Schistosoma mansoni, S. haematobium orS. japonicum (Deelder et al. (1996) Parasitology 112: 21-35); a multipleantigen peptide (MAP) composed of two distinct protective antigensderived from the parasite Schistosoma mansoni (Ferru et al. (1997)Parasite Immunol. 19: 1-11); Leishmania parasite surface molecules(Lezama-Davila (1997) Arch. Med. Res. 28: 47-53); third-stage larval(L3) antigens of L. loa (Akue et al. (1997) J Infect. Dis. 175: 158-63);the genes, Tams 1-1 and Tams 1-2, encoding the 30- and 32-kDa majormerozoite surface antigens of Theileria annulata (Ta) (d'Oliveira et al.(1996) Gene 172: 33-39); Plasmodium falciparum merozoite surface antigen1 or 2 (al-Yaman et al. (1995) Trans. R. Soc. Trop. Med. Hyg. 89:555-559; Beck et al. (1997) J Infect. Dis. 175: 921-926; Rzepczyk et al.(1997) Infect. Immun. 65: 1098-1100); circurnsporozoite (CS)protein-based B-epitopes from Plasmodium berghei, (PPPPNPND)2 andPlasmodium yoelii, (QGPGAP)3QG, along with a P. berghei T-helper epitopeKQIRDSITEEWS (Reed et al. (1997) Vaccine 15: 482-488); NYVAC-Pf7 encodedPlasmodium falciparum antigens derived from the sporozoite(circumsporozoite protein and sporozoite surface protein 2), liver(liver stage antigen 1), blood (merozoite surface protein 1, serinerepeat antigen, and apical membrane antigen 1), and sexual (25-kDasexual-stage antigen) stages of the parasite life cycle were insertedinto a single NYVAC genome to generate NYVAC-Pf7 (Tine et al. (1996)Infect. Immun. 64: 3833-3844); Plasmodium falciparum antigen Pfs230(Williamson et al. (1996) Mol. Biochem. Parasitol. 78: 161-169);Plasmodium falciparum apical membrane antigen (AMA-1) (Lal et al. (1996)Infect. Immun. 64: 1054-1059); Plasmodium falciparum proteins Pfs28 andPfs25 (Duffy and Kaslow (1997) Infect. Immun. 65: 1109-1113); Plasmodiumfalciparum merozoite surface protein, MSP1 (Hui et al. (1996) Infect.Immun. 64: 1502-1509); the malaria antigen Pf332 (Ahlborg et al. (1996)Immunology 88: 630-635); Plasmodium falciparum erythrocyte membraneprotein I (Baruch et al. (1995) Proc. Nat'l. Acad. Sci. USA 93:3497-3502; Baruch et al. (1995) Cell 82: 77-87); Plasmodium falciparummerozoite surface antigen, PfMSP-1 (Egan et al. (1996) J Infect. Dis.173: 765-769); Plasmodium falciparum antigens SERA, EBA-175, RAP1 andRAP2 (Riley (1997) J Pharm. Pharmacol. 49: 21-27); Schistosoma japonicumparamyosin (Sj97) or fragments thereof (Yang et al. (1995) Biochem.Biophys. Res. Commun. 212: 1029-1039); and Hsp70 in parasites (Marescaand Kobayashi (1994) Experientia 50: 1067-1074).

2.9.6. Contraception

Genetic vaccines that contain optimized antigens obtained by the methodsof the invention are also useful for contraception. For example, geneticvaccines can be obtained that encode sperm cell specific antigens, andthus induce anti-sperm immune responses. Vaccination can be achieved by,for example, administration of recombinant bacterial strains, e.g.Salmonella and the like, which express sperm antigen, as well as byinduction of neutralizing anti-hCG antibodies by vaccination by DNAvaccines encoding human chorionic gonadotropin (hCG), or a fragmentthereof.

Sperm antigens which can be used in the genetic vaccines include, forexample, lactate dehydrogenase (LDH-C4), galactosyltransferase (GT),SP-10, rabbit sperm autoantigen (RSA), guinea pig (g)PH-20, cleavagesignal protein (CS-1), HSA-63, human (h)PH-20, and AgX-1 (Zhu and Naz(1994) Arch. Androl. 33: 141-144), the synthetic spenn peptide, P10G(O'Rand et al. (1993) J Reprod. Immunol. 25: 89-102), the 135 kD, 95 kD,65 kD, 47 kD, 41 kD and 23 kD proteins of sperm, and the FA-1 antigen(Naz et al. (1995) Arch. Androl. 35: 225-231), and the 35 kD fragment ofcytokeratin 1 (Lucas et al. (1996) Anticancer Res. 16: 2493-2496).

The methods of the invention can also be used to obtain genetic vaccinesthat are expressed specifically in testis. For example, polynucleotidesequences that direct expression of genes that are specific to testiscan be used (e.g., fertilization antigen-1 and the like). In addition tosperm antigens, antigens expressed on oocytes or hormones regulatingreproduction may be useful targets of contraceptive vaccines. Forexample, genetic vaccines can be used to generate antibodies againstgonadotropin releasing hormone (GnRH) or zona pellucida proteins (Milleret al. (1997) Vaccine 15:1858-1862). Vaccinations using these moleculeshave been shown to be efficacious in animal models (Miller et al. (1997)Vaccine 15:1858-1862). Another example of a useful component of agenetic contraceptive vaccine is the ovarian zona pellucida glycoproteinZP3 (Tung et al. (1994) Reprod Fertil. Dev. 6:349-355).

2.10. Malarial Antigens and Vaccines

The present invention generally relates to the Plasmodium falciparumerythrocyte membrane protein 1 (“PfEMP1”), nucleic acids which encodePfEMP1, and antibodies which specifically recognize PfEMP1. Thepolypeptides, antibodies and nucleic acids are useful in a variety ofapplications including therapeutic, prophylactic, including vaccination,diagnostic and screening applications.

The data described herein, indicates that PfEMP1 is responsible for bothantigenic variation and receptor properties on PE, both of which arecentral to the special virulence and pathology of P. falciparum. Thecentral role of PfEMP1 in P. falciparum biology, as the malarialadherence receptor for host proteins on microvascular endothelium, asdescribed herein, indicates its usefulness in a malaria vaccine, inmodelling prophylactic drugs, and also as a target for therapeutics toreverse PE adherence in acute cerebral malaria (Howard and Gilladoga,1989).

2.10.1. Malarial Polypeptides

Soluble PfEMP1 has been reported to bind to CD36, TSP and ICAM-1, andtryptic fragments of PfEMP1 cleaved from the PE surface have been shownto bind to TSP or CD36 (Baruch, et al., Molecular Parasitology Meetingat Woods Hole, Sep. 18-22, 1994). Accordingly, in one aspect, thepresent invention provides substantially pure PfEMP1 polypeptides,analogs or biologically active fragments thereof.

The terms “substantially pure” or “isolated” refer, interchangeably, toproteins, polypeptides and nucleic acids which are separated fromproteins or other contaminants with which they are naturally associated.A protein or polypeptide is considered substantially pure when thatprotein makes up greater than about 50% of the total protein content ofthe composition containing that protein, and typically, greater thanabout 60% of the total protein content. More typically, a substantiallypure protein will make up from about 75 to about 90% of the totalprotein. Preferably, the protein will make up greater than about 90%,and more preferably, greater than about 95% of the total protein in thecomposition.

The term “biologically active fragment” as used herein, refers toportions of the proteins or polypeptides, e.g., a PfEMP1 derivedpolypeptide, which portions possess a particular biological activity,e.g., one or more activities found in a full length PfEMP1 polypeptide.For example, such biological activity may include the ability to bind aparticular protein, substrate or ligand, to elicit antibodies reactivewith PE, PfEMP1, the recombinant proteins or fragments thereof, toblock, reverse or otherwise inhibit an interaction between two proteins,between an enzyme and its substrate, between an epitope and an antibody,or may include a particular catalytic activity. With regard to thepolypeptides of the present invention, particularly preferredpolypeptides or biologically active fragments include, e.g.,polypeptides that possess one or more of the biological activitiesdescribed above, such as the ability to bind a ligand of PfEMP1 orinhibit the binding of PfEMP1 to one or more of its ligands, e.g., CD36,TSP, ICAM-1, VCAM-1, ELAM-1, Chondroitin sulfate or by the presencewithin the polypeptide fragment of antigenic determinants which permitthe raising of antibodies to that fragment.

The polypeptides of the present invention may also be characterized bytheir immunoreactivity with antibodies raised against PfEMP1 proteins orpolypeptides. In particularly preferred aspects, the polypeptides arecapable of inhibiting an interaction between a PfEMP1 protein and anantibody raised against a PfEMP1 protein. Additionally or alternatively,such fragments may be specifically immunoreactive with an antibodyraised against a PfEMP1 protein. Such fragments are also referred toherein as “immunologically active fragments.” Generally, suchbiologically active fragments will be from about 5 to about 500 aminoacids in length.

Typically, these peptides will be from about 20 to about 250 amino acidsin length, and preferably from about 50 to about 200 amino acids inlength. Generally, the length of the fragment may depend, in part, uponthe application for which the particular peptide is to be used. Forexample, for raising antibodies, the peptides may be of a shorterlength, e.g., from about 5 to about 50 amino acids in length, whereasfor binding applications, the peptides may have a greater length, e.g.,from about 50 to about 500 amino acids in length, preferably, from about100 to about 250 amino acids in length, and more preferably, from about100 to about 200 amino acids in length.

The polypeptides of the present invention may generally be preparedusing recombinant or synthetic methods well known in the art.Recombinant techniques are generally described in Sambrook, et al.,Molecular Cloning: A Laboratory Manual, (2nd ed.) Vols. 1-3, Cold SpringHarbor Laboratory, (1989). Techniques for the synthesis of polypeptidesare generally described in Merrifield, J. Amer. Chem. Soc. 85:2149-2456(1963), Atherton, et al., Solid Phase Peptide Synthesis: A PracticalApproach, IRL Press (1989), and, Merrifield, Science 232:341-347 (1986).

In preferred aspects, the polypeptides of the present invention may beexpressed by a suitable host cell that has been transfected with anucleic acid of the invention, as described in greater detail below.Isolation and purification of the polypeptides of the present inventioncan be carried out by methods that are generally well known in the art.For example, the polypeptides may be purified using readily availablechromatographic methods, e.g., ion exchange, hydrophobic interaction,HPLC or affinity chromatography, to achieve the desired purity. Affinitychromatography may be particularly attractive in allowing theinvestigator to take advantage of the specific biological activity ofthe desired peptide, e.g., ligand binding, presence of antigenicdeterminants, or the like.

Exemplary polypeptides of the present invention will generally comprisean amino acid sequence that is substantially homologous to the aminoacid sequence of a PfEMP1 protein, or biologically active fragmentsthereof, or may include sequences that may take on a homologousconformation. In particularly preferred aspects, the polypeptides of thepresent invention will comprise an amino acid sequence that issubstantially homologous to the amino acid sequence shown, described&/or referenced herein (including incorporated by reference), or abiologically active fragment thereof.

By “substantially homologous” is meant an amino acid sequence which isat least about 50% homologous to the amino acid sequence of PfEMP1 or abiologically active fragment thereof, preferably at least about 90%homologous, and more preferably at least about 95% homologous. In someaspects, substantially homologous may include a sequence that is atleast 50% homologous, but that presents a homologous structure in threedimensions, i.e., includes a substantially similar surface charge orpresentation of hydrophobic groups.

Examples of preferred polypeptides include polypeptides having an aminoacid sequence substantially homologous to the MC PfEMP1 amino acidsequence as shown, described &/or referenced herein (includingincorporated by reference), and PfEMP1 of other P. falciparum strains asshown, described &/or referenced herein (including incorporated byreference), as well as biologically active fragments of thesepolypeptides. Preferred peptides include those peptide fragments ofPfEMP1 that are involved in the sequestration of parasitizederythrocytes. Examples of these preferred peptides include peptideswhich comprise an amino acid sequence which is substantially homologousto amino acids 576 through 755 of the PfEMP1 amino acid sequence shown,described &/or referenced herein (including incorporated by reference).

Also among the particularly preferred peptides of the present inventionare those peptides and peptide fragments of PfEMP1 which are relativelyconserved among the variant strains of P. falciparum or which containregions of high homology to PfEMP1 proteins from other strains. The term“relatively conserved” generally refers to amino acid sequences that aresubstantially homologous to portions of the amino acid sequence shown,described &/or referenced herein (including incorporated by reference).However, also included within the definition of this term are peptideswhich are encoded by a nucleic acid which is a PCR product of primerprobes, and particularly, universal primers, derived from the PfEMP1nucleic acid sequence. In particular, primer probes derived from thenucleic acid sequence shown, described &/or referenced herein (includingincorporated by reference), may be used to amplify nucleic acids fromother strains of P. falciparum. Particularly preferred primer sequencesinclude the primer sequences shown in Table 1, below. Similarly,universal primer compositions, described in greater detail below andalso shown in Table 1, may be used to amplify sequences that encode thepeptides of the present invention.

Specific examples of relatively conserved peptides include those thatare contained in a region of PfEMP1 proteins that corresponds to aminoacids 576 through 755 of the amino acid sequence of MC PfEMP1, as shown,described &/or referenced herein (including incorporated by reference).

Similar regions have been specifically elucidated in a number of P.falciparum strains (as described herein). In general, thesecorresponding regions may be described as containing amino acidsequences that are encoded by the universal primer sequences describedbelow. Generally, these amino acid sequences have one or more of thefollowing general structures:

TTIDKX₁LX₂HE and/or FFWX₃WVX₄X₅MLwhere X₁ is selected from leucine or isoleucine, X₂ is selected fromglutamine and asparagine, X₃ is selected from the methionine, lysine andaspartic acid, X₄ is selected from histidine, threanine and tyrosine andX₅ is selected from aspartic acid, glutamic acid and histidine. Inparticularly preferred aspects, the polypeptides may contain both of theabove general amino acid sequences. Particularly preferred amino acidsequences will possess the conserved amino acids shown in the variousfragments shown, described &/or referenced herein (includingincorporated by reference). In particular, conserved amino acidsequences of six amino acids or greater, shown, described &/orreferenced herein (including incorporated by reference), may be used asepitopes for generation of antibodies that cross react with multiple P.falciparum strains.

The peptides of the invention may be free or tethered, or may includelabeled groups for detection of the presence of the polypeptides.Suitable labels include radioactive, fluorescent and catalytic labelinggroups that are well known in the art and that are substantiallydescribed herein, e.g., signaling enzymes, chemical reporter groups,polypeptide signals, biotin and the like. Additionally, the peptides mayinclude modifications to the N and C-termini of the peptide, e.g., anacylated N-terminus or amidated C-terminus.

Also included within the present invention are amino acid variants ofthe above described polypeptides. These variants may include insertions,deletions and substitutions with other amino acids. For example, in someaspects, amino acids may be substituted with different amino acidshaving similar structural characteristics, e.g., net charge,hydrophobicity, or the like. For example, phenylalanine may besubstituted with tyrosine, as a similarly hydrophobic residue.Glycosylation modifications, either changed, increased amounts ordecreased amounts, as well as other sequence modifications are alsoenvisioned.

In addition to the above polypeptides which consist only ofnaturally-occurring amino acids, peptidomimetics of the polypeptides ofthe present invention are also provided. Peptide analogs are commonlyused in the pharmaceutical industry as non-peptide drugs with propertiesanalogous to those of the template peptide. These types of non-peptidecompound are termed “peptide mimetics” or “peptidomimetics” (Fauchere,J. (1986) Adv. Drug Res. 15:29; Veber and Freidinger (1985) TINS p. 392;and Evans et al. (1987) J. Med. Chem. 30:1229, and are usually developedwith the aid of computerized molecular modeling. Peptide mimetics thatare structurally similar to therapeutically useful peptides may be usedto produce an equivalent therapeutic or prophylactic effect. Generally,peptidomimetics are structurally similar to a paradigm polypeptide(i.e., a polypeptide that has a biological or pharmacological activity),such as naturally-occurring receptor-binding polypeptide, but have oneor more peptide linkages optionally replaced by a linkage selected fromthe group consisting of: —CH₂NH—, —CH₂S—, —CH₂—CH₂—, —CH═CH— (cis andtrans), —COCH₂—, —CH(OH)CH₂—, and —CH₂SO—, by methods known in the artand further described in the following references: Spatola, A. F. inChemistry and Biochemistry of Amino Acids, Peptides, and Proteins, B.Weinstein, eds., Marcel Dekker, New York, p. 267 (1983); Spatola, A. F.,Vega Data (March 1983), Vol. 1, Issue 3, “Peptide BackboneModifications” (general review); Morley, J. S., Trends Pharm Sci (1980)pp. 463-468 (general review); Hudson, D. et al., Int J Pept Prot Res(1979) 14:177-185 (—CH₂NH—, CH₂CH₂—); Spatola, A. F. et al., Life Sci(1986) 38:1243-1249 (—CH₂—S); Hann, M. M., J Chem Soc Perkin Trans I(1982) 307-314 (—CH—CH—, cis and trans); Almquist, R. G et al., J MedChem (1980) 23:1392-1398 (—COCH₂—); Jennings-White, C. et al.,Tetrahedron Lett (1982) 23:2533 (—COCH₂—); Szelke, M. et al., EuropeanAppln. EP 45665 (1982) CA: 97:39405 (1982) (—CH(OH)CH₂—); Holladay, M.W. et al., Tetrahedxon Lett (1983) 24:4401-4404 (—C(OH)CH₂—); and Hruby,V. J., Life Sci (1982) 31:189-199 (—CH₂—S—). Peptide mimetics may havesignificant advantages over polypeptide embodiments, including, forexample: more economical production, greater chemical stability,enhanced pharmacological properties (half-life, absorption, potency,efficacy, etc.), altered specificity (e.g., a broad-spectrum ofbiological activities), reduced antigenicity, and others.

Labeling of peptidomimetics usually involves covalent attachment of oneor more labels, directly or through a spacer (e.g., an amide group), tonon-interfering position(s) on the peptidomimetic that are predicted byquantitative structure-activity data and/or molecular modeling. Suchnon-interfering positions generally are positions that do not formdirect contacts with the molecules to which the peptidomimetic binds(e.g., CD36) to produce the therapeutic effect. Derivitization (e.g.,labeling) of peptidomimetics should not substantially interfere with thedesired biological or pharmacological activity of the peptidomimetic.Generally, peptidomimetics of peptides of the invention bind to theirligands (e.g., CD36) with high affinity and possess detectablebiological activity (i.e., are agonistic or antagonistic to one or moreligand-mediated phenotypic changes).

Systematic substitution of one or more amino acids of a consensussequence with a D-amino acid of the same type (e.g., D-lysine in placeof L-lysine) may be used to generate more stable peptides. In addition,constrained peptides comprising a consensus sequence or a substantiallyidentical consensus sequence variation may be generated by methods knownin the art (Rizo and Gierasch (1992) Ann. Rev. Biochem. 61: 387; forexample, by adding internal cysteine residues capable of formingintramolecular disulfide bridges which cyclize the peptide.

Polypeptides of the present invention may also be characterized by theirability to bind antibodies raised against PfEMP1, or fragments thereof.Preferably, these antibodies recognize polypeptide domains that arehomologous to the PfEMP1 proteins from a number of variants of P.falciparum. These homologous domains will generally be presentthroughout the family of PfEMP1 proteins. A variety of immunoassayformats may be used to select antibodies specifically immunoreactivewith a particular protein or domain. For example, solid-phase ELISAimmunoassays are routinely used to select monoclonal antibodiesspecifically immunoreactive with a protein. See Harlow and Lane (1988)Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, NewYork, for a description of immunoassay formats and conditions that canbe used to determine specific immunoreactivity. Antibodies to PfEMP1 andits fragments are discussed in greater detail, below. As used herein,the terms “polypeptide” or “peptide” are used interchangeably to referto peptides, peptidomimetics, analogs, and the like, as described above.

The polypeptides of the present invention may be used as isolatedpolypeptides, or may exist as fusion proteins. A “fusion protein”generally refers to a composite protein made up of two or more separate,heterologous proteins which are normally not fused together as a singleprotein.

Thus, a fusion protein may comprise a fusion of two or more heterologousor homologous sequences, provided these sequences are not normally fusedtogether. Fusion proteins will generally be made by either recombinantnucleic acid methods, i.e., as a result of transcription and translationof a gene fusion comprising a segment encoding a polypeptide comprisinga PfEMP1 protein and a segment which encodes one or more heterologousproteins, or by chemical synthesis methods well known in the art.

2.10.2. Malarial Nucleic Acids and Cells Capable of Expressing Same

Also provided in the present invention are isolated nucleic acidsequences which encode the above described polypeptides and biologicallyactive fragments. Typically, such nucleic acid sequences will comprise asegment that is substantially homologous to a portion or fragment of thenucleic acid sequence shown, described &/or referenced herein (includingincorporated by reference). Preferably, the nucleic acids of the presentinvention will comprise at least about 15 consecutive nucleotides of thenucleic acid, more preferably, at least about 20 contiguous nucleotides,still more preferably, at least about 30 contiguous nucleotides, andstill more preferably, at least about 50 contiguous nucleotides from thenucleotide sequence.

Substantial homology in the nucleic acid context means that thesegments, or their complementary strands, when compared, are the samewhen properly aligned with the appropriate nucleotide insertions ordeletions, in at least about 60% of the nucleotides, typically, at leastabout 70%, more typically, at least about 80%, usually, at least about90%, and more usually, at least about 95% to 98% of the nucleotides.Alternatively, substantial homology exists when the segments willhybridize under selective hybridization conditions to a strand, or itscomplement, typically using a sequence of at least about 15 contiguousnucleotides derived from the PfEMP1 nucleic acid sequence. However,larger segments will usually be preferred, e.g., at least about 20contiguous nucleotides, more usually about 40 contiguous nucleotides,and preferably more than about 50 contiguous nucleotides. Selectivehybridization exists when hybridization occurs which is more selectivethan total lack of specificity. See, Kanchisa, Nucleic Acid Res.12:203-213 (1984).

Nucleic acids of the present invention include RNA, cDNA, genomic DNA,synthetic forms and mixed polymers, both sense and antisense strands.Furthermore, different alleles of each isoform are also included. Thepresent invention also provides recombinant nucleic acids which are nototherwise naturally occurring. The nucleic acids included in the presentinvention will typically comprise RNA or DNA or mixed polymers. The DNAcompositions will generally include a coding region which encodes apolypeptide comprising an amino acid sequence substantially homologousto the amino acid sequence of a PfEMP1 protein. More preferred are thoseDNA segments comprising a nucleotide sequence which encodes a CD36binding fragment of the PfEMP1 protein.

cDNA encoding the polypeptides of the present invention, or fragmentsthereof, may be readily employed as a probe useful for obtaining geneswhich encode the PfEMP1 polypeptides of the present invention.Preparation of these probes may be carried out by generally well knownmethods. For example, the cDNA probes may be prepared from the aminoacid sequence of the PfEMP1 protein. In particular, probes may beprepared based upon segments of the amino acid sequence which possessrelatively low levels of degeneracy, i.e., few or one possible nucleicacid sequences which encode therefor.

Suitable synthetic DNA fragments may then be prepared, e.g., by thephosphoramidite method described by Beaucage and Carruthers, Tetra.Letts. 22:1859-1862 (1981). Alternatively, nucleotide sequences whichare relatively conserved among the PfEMP1 coding sequences for thevarious P. falciparum strains may be used as suitable probes. A doublestranded probe may then be obtained by either synthesizing thecomplementary strand and hybridizing the strands together underappropriate conditions or by adding the complementary strand using DNApolymerase with an appropriate primer sequence. Such cDNA probes may beused in the design of oligonucleotide probes and primers for screeningand cloning such genes, e.g., using well known PCR techniques, or,alternatively, may be used to detect the presence or absence of a PfEMP1gene in a cell. Such nucleic acids, or fragments may comprise part orall of the cDNA sequence that encodes the polypeptides of the presentinvention. Effective cDNA probes may comprise as few as 15 consecutivenucleotides in the cDNA sequence, but will often comprise longersegments. Further, these probes may further comprise an additionalnucleotide sequence, such as a transcriptional primer sequence forcloning, or a detectable group for easy identification and location ofcomplementary sequences.

cDNA or genomic libraries of various types may be screened for newalleles or related sequences using the above probes. The choice of cDNAlibraries normally corresponds to tissue sources which are abundant inmRNA for the desired polypeptides. Phage libraries are normallypreferred, e.g., λgt11, but plasmid or YAC libraries may also be used.Clones of a library are spread onto plates, transferred to a substratefor screening, denatured, and probed for the presence of the desiredsequences.

In a related aspect, the nucleic acids of the present invention alsoinclude the PCR product or RT-PCR product, produced using the abovedescribed primer probes. For example, primer probes derived from thenucleotide sequence shown, described &/or referenced herein (includingincorporated by reference), may be used to amplify sequences fromdifferent malaria parasites, and in particular, different strains of P.falciparum.

The nucleic acids of the present invention may be present in wholecells, cell lysates or in partially pure or substantially pure orisolated form. Such “substantially pure” or “isolated” forms of thesenucleic acids generally refer to the nucleic acid separated fromcontaminants with which it is generally associated, e.g., lipids,proteins and other nucleic acids. The nucleic acids of the presentinvention will be greater than about 50% pure. Typically, the nucleicacids will be more than about 60% pure, more typically, from about 75%to about 90% pure, and preferably, from about 95% to about 98% pure.

The present invention also provides substantially similar nucleic acidsequences, allelic variations and natural or induced sequences of theabove described nucleic acids, as well as chemically modified andsubstituted nucleic acids, e.g., those which incorporate modifiednucleotide bases or which incorporate a labeling group. In addition tocomprising a segment which encodes a PfEMP1 protein or fragment thereof,the nucleic acids of the present invention may also comprise a segmentencoding a heterologous protein, such that the gene is expressed toproduce the two proteins as a fusion protein, as substantially describedabove.

In addition to their use as probes, the nucleic acids of the presentinvention may also be used in the preparation of the polypeptides of thepresent invention, as described above. DNA encoding the polypeptides ofthe present invention will typically be incorporated into DNA constructscapable of introduction to and expression in an in vitro cell culture.Often, the nucleic acids of the present invention may be used to producea suitable recombinant host cell.

Specifically, DNA constructs will be suitable for replication in aunicellular host, such as bacteria, e.g., E. coli, viruses or yeast, butmay also be intended for introduction into a cultured mammalian, plant,insect, or other eukaryotic cell lines. DNA constructs prepared forintroduction into bacteria or yeast will typically include a replicationsystem recognized by the host, the intended DNA segment encoding thedesired polypeptide, transcriptional and translational initiation andtermination regulatory sequences operably linked to the polypeptideencoding segment. A DNA segment is operably linked when it is placedinto a functional relationship with another DNA segment. For example, apromoter or enhancer is operably linked to a coding sequence if itstimulates the transcription of the sequence; DNA for a signal sequenceis operably linked to DNA encoding a polypeptide if it is expressed as apreprotein that participates in the secretion of the polypeptide.Generally, DNA sequences that are operably linked are contiguous, and inthe case of a signal sequence both contiguous and in reading phase.However, enhancers need not be contiguous with the coding sequenceswhose transcription they control. Linking is accomplished by ligation atconvenient restriction sites or at adapters or linkers inserted in lieuthereof. The selection of an appropriate promoter sequence willgenerally depend upon the host cell selected for the expression of theDNA segment.

Examples of suitable promoter sequences include prokaryotic, andeukaryotic promoters well known in the art. See, e.g., Sambrook et al.,supra. The transcriptional regulatory sequences will typically include aheterologous enhancer or promoter which is recognized by the host. Theselection of an appropriate promoter will depend upon the host, butpromoters such as the trp, lac and phage promoters, tRNA promoters andglycolytic enzyme promoters are known and available. See Sambrook etal., supra.

Conveniently available expression vectors which include the replicationsystem and transcriptional and translational regulatory sequencestogether with the insertion site for the PfEMP1 polypeptide encodingsegment may be employed. Examples of workable combinations of cell linesand expression vectors are described in Sambrook et al., supra, and inMetzger et al., Nature 334:31-36 (1988).

The vectors containing the DNA segments of interest, e.g., thoseencoding polypeptides comprising a PfEMP1 protein or fragments thereof,can be transferred into the host cell by well known methods, which mayvary depending upon the type of host used. For example, calcium chloridetransfection is commonly used for prokaryotic cells, whereas calciumphosphate treatment may be used for other hosts. See, Sambrook et al.,supra. The term “transformed cell” as used herein, includes the progenyof originally transformed cells.

Techniques for manipulation of nucleic acids which encode thepolypeptides of the present invention, i.e., subcloning the nucleicacids into expression vectors, labeling probes, DNA hybridization andthe like, are generally described in Sambrook, et al., supra. Inrecombinant methods, generally the nucleic acid encoding a peptide ofthe present invention is first cloned or isolated in a form suitable forligation into an expression vector. After ligation, the vectorscontaining the nucleic acids fragments or inserts are introduced into asuitable host cell, for the expression of the polypeptide of theinvention. The polypeptides may then be purified or isolated from thehost cells. Methods for the synthetic preparation of oligonucleotidesare generally described in Gait, oligonucleotide Synthesis: A PracticalApproach, IRL Press (1990).

There are various methods of isolating the nucleic acids which encodethe polypeptides of the present invention. Typically, the DNA isisolated from a genomic or cDNA library using labeled oligonucleotideprobes specific for sequences in the desired DNA. Restrictionendonuclease digestion of genomic DNA or cDNA containing the appropriategenes can be used to isolate the DNA encoding the binding domains ofthese proteins. From the PfEMP1 sequence given (as shown herein), apanel of restriction endonucleases can be constructed to give cleavageof the DNA in desired regions, i.e., to obtain segments which encodebiologically active fragments of the PfEMP1 protein. Followingrestriction endonuclease digestion, DNA encoding the polypeptides of thepresent invention is identified by its ability to hybridize with anucleic acid probe in, for example a Southern blot format. These regionsare then isolated using standard methods. See, e.g., Sambrook, et al.,supra.

The polymerase chain reaction, or “PCR” can also be used to preparenucleic acids which encode the polypeptides of the present invention.PCR technology is used to amplify nucleic acid sequences of the desirednucleic acid, e.g., the DNA which encodes the polypeptides of theinvention, directly from mRNA, cDNA, or genomic or cDNA libraries.

Appropriate primers and probes for amplifying the nucleic acidsdescribed herein, may be generated from analysis of the PfEMP1oligonucleotide sequence, such as those shown, described &/or referencedherein (including incorporated by reference) and Table 1. Briefly,oligonucleotide primers complementary to the two 31 borders of the DNAregion to be amplified are synthesized. The PCR is then carried outusing the two primers. See, e.g., PCR Protocols: A Guide to Methods andApplications (Innis, M., Gelfand, D., Sninsky, J. and White, T., eds.)Academic Press (1990). Primers can be selected to amplify various sizedsegments from the PfEMP1 oligonucleotide sequence. The primers may alsocontain a restriction site and additional bases to permit “in-frame”cloning of the insert into an appropriate expression vector, using therestriction sites present on the primers.

2.10.3. Antibodies

The nucleic acids and polypeptides of the present invention, orfragments thereof, are also useful in producing antibodies, eitherpolyclonal or monoclonal. These antibodies are produced by immunizing anappropriate vertebrate host, e.g., rat, mouse, rabbit or goat, with apolypeptide of the invention, or its fragment, or plasmid DNA containinga nucleic acid of the invention, alone or in conjunction with anadjunct. Usually, two or more immunizations are involved, and a few daysfollowing the last injection, the blood or spleen of the host will beharvested.

For production of polyclonal antibodies, an appropriate target immunesystem is selected, typically a mouse or rabbit, but also includinggoats, sheep, cows, guinea pigs, monkeys and rats. The substantiallypurified antigen or plasmid is presented to the immune system in afashion determined by methods appropriate for the animal. These andother parameters are well known to immunologists. Typically, injectionsare given in the footpads, intramuscularly, intradermally orintraperitoneally. The immunoglobulins produced by the host can beprecipitated, isolated and purified by routine methods, includingaffinity purification.

For monoclonal antibodies, appropriate animals will be selected and thedesired immunization protocol followed. After the appropriate period oftime, the spleens of these animals are excised and individual spleencells are fused, typically, to immortalized myeloma cells underappropriate selection conditions. Thereafter, the cells are clonallyseparated and the supernatants of each clone are tested for theproduction of an appropriate antibody specific for the desired region ofthe antigen. Techniques for producing antibodies are well known in theart. See, e.g., Goding et al., Monoclonal Antibodies: Principles andPractice (2d ed.) Acad. Press, N.Y., and Harlow and Lane, Antibodies: ALaboratory Manual, Cold Spring Harbor Laboratory, New York (1988). Othersuitable techniques involve the in vitro exposure of lymphocytes to theantigenic polypeptides or alternatively, to selection of libraries ofantibodies in phage or similar vectors. Huse et al., Generation of LargeCombinatorial Library of the Immunoglobulin Repertoire in Phage Lambda,Science 246:1275-1281 (1989). Monoclonal antibodies with affinities of10⁸ liters/mole, preferably 10⁹ to 10¹⁰ or stronger, will be produced bythese methods.

The antibodies generated can be used for a number of purposes, e.g., asprobes in immunoassays, for inhibiting PfEMP1 binding to its ligands,thereby inhibiting or reducing erythrocyte sequestration, in diagnosticsor therapeutics, or in research to further elucidate the mechanism ofvarious aspects of malarial infection, and particularly, P. falciparuminfection. The antibodies of the present invention can be used with orwithout modification. Frequently, the antibodies will be labeled byjoining, either covalently or non-covalently, a substance which providesfor a detectable signal. Such labels include those that are well knownin the art, such as the labels described previously for the polypeptidesof the invention. Additionally, the antibodies of the invention may bechimeric, human-like or humanized, in order to reduce their potentialantigenicity, without reducing their affinity for their target.Chimeric, human-like and humanized antibodies have generally beendescribed in the art. Generally, such chimeric, human-like or humanizedantibodies comprise variable regions, e.g., complementarity determiningregions (CDR) (for humanized antibodies), from a mammalian animal, i.e.,a mouse, and a human framework region. By incorporating as littleforeign sequence as possible in the hybrid antibody, the antigenicity isreduced. Preparation of these hybrid antibodies may be carried out bymethods well known in the art.

Preferred antibodies are those that are specifically immunoreactive withthe polypeptides of the present invention and their immunologicallyactive fragments. The phrase “specifically immunoreactive,” whenreferring to the interaction between an antibody of the invention and aparticular protein, refers to an antibody that specifically recognizesand binds with relatively high affinity to the particular protein, suchthat this binding is determinative of the presence of the protein in aheterogeneous population of proteins and other biologics. Thus, underdesignated immunoassay conditions, the specified antibodies bind to aparticular protein and do not bind in a significant amount to otherproteins present in the sample. A variety of immunoassay formats may beused to select antibodies specifically immunoreactive with a particularprotein. For example, solid-phase ELISA immunoassays are routinely usedto select monoclonal antibodies specifically immunoreactive with aprotein. See Harlow and Lane (1988) Antibodies, A Laboratory Manual,Cold Spring Harbor Publications, New York, for a description ofimmunoassay formats and conditions that can be used to determinespecific immunoreactivity.

The antibodies generated can be used for a number of purposes, e.g., asprobes in immunoassays, for inhibiting interaction between a PfEMP1protein and its ligand, e.g., CD-36, TSP, ICAM-1, VCAM-1, ELAM-1, orChondroitin sulfate, thereby inhibiting or reducing the level ofPfEMP1-ligand interaction, in diagnostics or therapeutics, or inresearch to further elucidate the mechanism of malarial pathology, e.g.,erythrocyte sequestration. Where the antibodies are used to block orreverse the interaction between a polypeptide of the invention and anassociating ligand or PE, the antibody will generally be referred to asa “blocking antibody.” Preferred antibodies are those monoclonal orpolyclonal antibodies which specifically recognize and bind thepolypeptides of the invention. Accordingly, these preferred antibodieswill specifically recognize and bind the polypeptides which have anamino acid sequence that is substantially homologous to the relevantamino acid sequence shown, described &/or referenced herein (includingincorporated by reference), or immunologically active fragments thereof.Still more preferred are antibodies which are capable of forming anantibody-ligand complex with the relatively conserved polypeptidefragments of PfEMP1 sequences, and are thereby capable of blocking aninteraction of PfEMP1 from a variety of P. falciparum strains, andPfEMP1 ligands.

2.10.4. Methods of Use

The polypeptides, antibodies, and nucleic acids of the present inventionhave a variety of important uses, including, but not limited to,diagnostic, screening, prophylactic, including vaccination, andtherapeutic applications.

2.10.4.1. Diagnostic Applications

In a particularly preferred aspect, the present invention providesmethods and reagents useful in detecting the presence of PfEMP1 in asample. These detection methods are particularly useful in diagnosingmalarial infections in a patient. For example, in a particularlypreferred aspect, the antibodies of the present invention may be used toassay for the presence or absence of PfEMP1 in a sample. Immunoassaytechniques for the detection of the particular antigen are very wellknown in the art. For a review of immunological and immunoassayprocedures in general, see Basic and Clinical Immunology 7th Edition (D.Stites and A. Terr ed.) 1991.

Moreover, the immunoassays of the present invention can be performed inany of several configurations, which are reviewed extensively in EnzymeImmunoassay, E. T. Maggio, ed., CRC Press, Boca Raton, Fla. (1980);“Practice and Theory of Enzyme Immunoassays,” P. Tijssen, LaboratoryTechniques in Biochemistry and Molecular Biology, Elsevier SciencePublishers B.V. Amsterdam (1985); and, Harlow and Lane, Antibodies, ALaboratory Manual, supra. Generally, these methods comprise contactingthe antibody with a sample to be tested, and detecting any specificbinding between the antibody and a protein within the sample. Typically,this will be in a blot format, e.g., western blot, or in an ELISAformat. Methods of performing these assay formats are well known in theart. See, e.g., Basic and Clinical Immunology, 7th ed. (D. Stites and ATerr, eds., 1991).

Typically, these diagnostic methods comprise contacting a sample with anantibody to PfEMP1, as described herein, and determining whether theantibody binds to any portion of the sample. In the case of humandiagnostic techniques, the sample may be a whole blood sample, or somefraction thereof, e.g. an erythrocyte containing sample. Generally, suchdiagnostic methods are well known in the art, and are described in theabove described references. The immunoreactivity of the antibody withthe sample, indicates the presence of PfEMP1 in the sample, and, in thecase of a sample derived from a patient, a possible malarial infection.

Alternatively, labeled polypeptides of the present invention may be usedas diagnostic reagents in detecting the presence or absence ofantibodies to PfEMP1, in a patient. The presence of antibodies within apatient would be indicative that the patient had been exposed to amalaria parasite sufficiently to result in an antigenic response.

Similarly, the nucleic acid probes of the invention may be used in asimilar manner, i.e., to identify the presence in a sample of a DNAsegment encoding a PfEMP1 polypeptide, or as PCR or RT-PCR primers toamplify and then detect PfEMP1 encoding nucleic acid segments. Suchassays typically involve the immobilization of nucleic acids in thesample, followed by interrogation of the immobilized sequences with achemically labeled oligonucleotide probe, as described herein.Hybridization of the probe to the immobilized sample indicates thepresence of a DNA segment encoding PfEMP1, and thus, a malarialinfection. As described above, assays may be further designed toindicate not only the presence of a Malarial parasite, but also indicatethe strain of parasite present. Although described in terms of animmobilized sample probed with a solution based oligonucleotide probe, awide variety of assay conformations may be adopted, which conformationsare generally well known in the art.

2.10.4.2. Screening Applications

In another particularly preferred aspect, the present invention providesmethods for screening compounds to determine whether or not theparticular compound is an antagonist of a symptom of a malarialinfection. In particular, the screening methods of the present inventioncan be used to determine whether a test compound is an antagonist of thesequestration of erythrocytes which is associated with P. falciparummalaria. More particularly, the screening methods can determine whethera compound is an antagonist of the PfEMP1/ligand interaction. Ligands ofPfEMP1 generally include, e.g., CD36, TSP, ELAM-1, ICAM-1, VCAM-1 orChondroitin sulfate.

Generally, the screening methods of the present invention comprisecontacting PfEMP1 protein, or a fragment thereof, and/or ligand protein,with a compound which is to be screened (“test compound”). The level ofPfEMP1/ligand complex formed may then be detected and compared to acontrol, e.g., in the absence of the test compound. A decrease in thelevel of PfEMP1/ligand interaction is indicative that the test compoundis an antagonist of that interaction.

A test compound may be a chemical compound, a mixture of chemicalcompounds, a biological macromolecule, or an extract made frombiological materials, such as bacteria, phage, yeast, plants, fungi,animal cells or tissues. Test compounds are evaluated for potentialactivity as antagonists of PfEMP1/ligand interaction by inclusion in thescreening assays described herein. An “antagonist” refers to a compoundwhich will diminish the level of PfEMP1/ligand interaction, over acontrol.

It will often be desirable in the screening assays of the presentinvention, to provide one of the PfEMP1 or ligand proteins immobilizedon a solid support. Suitable solid supports include, e.g., agarose,cellulose, dextran, Sephadex, Sepharose, carboxymethyl cellulose,polystyrene, filter paper, nitrocellulose, ion exchange resins, plasticfilms, glass beads, polyaminemethylvinylether maleic acid copolymer,amino acid copolymer, ethylene-maleic acid copolymer, nylon, silk, etc.The support may be in the form of, e.g., a test tube, microtiter plate,beads, test strips, flat surface, e.g., for blotting formats, or thelike. The reaction of the PfEMP1 polypeptide or its ligand with theparticular solid support may be carried out by methods well known in theart, e.g., binding to an immobilized anti-PfEMP1 antibody, or binding toprederivatized solid support.

In addition to the foregoing, it may also be desirable to provide eitherthe PfEMP1 or its ligand linked to a suitable detectable group to makedetection of binding of one protein to the other, simpler. Usefuldetectable groups, or labels, are generally well known in the art. Forexample, a detectable group may be a radiolabel, such as, ¹²⁵I, ³²P or³⁵S, or a fluorescent or chemiluminescent group.

Alternatively, the detectable group may be a substrate, cofactor,inhibitor, affinity ligand, antibody binding epitope tag, or an enzymewhich is capable of being assayed. Suitable enzymes include, e.g.,horseradish peroxidase, luciferase, or another readily assayableenzymes. These enzyme groups may be attached to the PfEMP1 polypeptide,or its ligand by chemical means or may be expressed as a fusion protein,as already described.

Generally, where one of the above proteins, e.g., the PfEMP1 ligand, isimmobilized on a solid support, the other protein, e.g., PfEMP1 or itsfragment, will be labeled with an appropriate detectable group. Assayingwhether a compound is an antagonist of the interaction of the twoproteins is then a matter of contacting the labeled PfEMP1 polypeptideor fragment with the immobilized ligand, in the presence of the testcompound, under conditions which allow specific binding of the twoproteins. The amount of label bound to the solid support is compared toa control, where no test compound was added. Where a test compoundresults in a reduction of the amount of label which binds to a solidsupport, that compound is an antagonist of the PfEMP1/ligandinteraction.

2.10.4.3. Therapeutic and Prophylactic Applications

In addition to the above described uses, the polypeptides of the presentinvention may also be used in therapeutic applications, for thetreatment of human and/or non-human mammalian patients. The therapeuticuses of the polypeptides of the present invention include the treatmentof symptoms of existing disorders, as well as prophylactic applications.The term “prophylactic” refers to the prevention of a particulardisorder, or symptoms of a particular disorder. Thus, prophylactictreatments will generally include drugs which actively participate inthe prevention of a particular disorder such as a malaria infection, orsymptoms thereof. Prophylactic applications will also include treatmentswhich elicit a preventative response from a patient, including, forexample, an immunological response as in the case of vaccination.

Typically, both therapeutic and prophylactic applications will compriseadministering an effective amount of the compositions of the presentinvention to a patient, to treat or prevent symptoms, or the onset of amalarial parasite infection. An “effective amount”, as the term is usedherein, is defined as the amount of the composition which is necessaryto achieve the desired goal, i.e. alleviation of symptoms, prevention ofsymptoms or infection, or treatment of disease.

In prophylactic applications, the polypeptides of the present inventionmay be used in a variety of treatments. For example, the polypeptides ofthe invention are particularly useful as a vaccine, to elicit animmunological response by a patient, e.g., production of antibodiesspecific for PfEMP1. In particular, such vaccine applications generallyinvolve the administration of the PfEMP1 protein or biologically activefragments thereof, to the host or patient.

In response to this administration, the patient's immune system willgenerate antibodies to the particular PfEMP1 protein or fragmentintroduced. An amount of the polypeptides sufficient to produce animmunological response in a patient is termed “an immunogenicallyeffective amount.” Thus, the vaccines of the present invention willcontain an immunogenically effective amount of the polypeptides of thepresent invention. The immune response of the patient may includegeneration of antibodies, activation of cytotoxic T-lymphocytes againstcells expressing the polypeptides, e.g., PE, or other mechanisms knownto the skilled artisan. See, e.g., Paul, Fundamental Immunology, 2dEdition, Raven Press. Useful carriers are well known in the art, andinclude for example, thyroglobulin, albumins such as human serumalbumin, tetanus toxoid, polyamino acids such as poly(D-lysine;D-glutamic acid), influenza, hepatitis B virus core protein, hepatitis Bvirus recombinant vaccine. The vaccines can also contain aphysiologically tolerable diluent, such as water, buffered water,buffered saline, saline and typically may further include an adjuvant,such as incomplete Freunds adjuvant, aluminum phosphate, aluminumhydroxide, alum, or other materials well known in the art.

Alternatively, the nucleic acids of the present invention may also beused as vaccines for the prevention of malaria symptoms, and/orinfection by malaria parasites. See Sedegah, et al. Proc. Nat'l Acad.Sci. (1994) 91:9866-9870.

For example, plasmid DNA comprising the nucleic acids of the presentinvention may be directly administered to a patient. Expression of this“naked” DNA will have effects similar to the injection of the actualpolypeptides, as described above. Specifically, the patient's immuneresponse to the presence of the proteins expressed from the DNA, willresult in the production of antibodies to that protein. The nucleicacids may also be used to design antisense probes to interrupttranscription of PfEMP1 peptides in parasitized erythrocytes.

Antisense methods are generally well known in the art. The polypeptidesof the present invention, and analogs thereof, may also be used asprophylactic treatments to prevent the onset of symptoms of malarialinfection. For example, administration of the polypeptides can directlyinhibit, block or reverse the sequestration of erythrocytes in patientssuffering from P. falciparuin malaria infections. In particular, thepolypeptides of the invention may be used to compete with or displace PEassociated PfEMP1 in binding CD36.

The blockage or reversal of sequestration will reduce or eliminate themicrovascular occlusion generally associated with the pathology of thistype of malaria, which, again, can lead to destruction of the PE by thehost. The antibodies of the invention may also be used in a similarfashion. In particular, the antibodies, which are capable of binding thepolypeptides of the present invention, may be directly administered to apatient. By binding PfEMP1, the antibodies of the present invention areeffective in blocking, reducing or reversing PfEMP1 mediatedinteractions, e.g., erythrocyte sequestration. Chimeric, human-like orhumanized antibodies are particularly useful for administration to humanpatients. Additionally, such antibodies may also be used as a passivevaccination method to provide a subject with a short term immunization,much as anti-hepatitis A injections have been used previously.

In alternative aspects, the polypeptides, antibodies and nucleic acidsof the invention may be used to treat a patient already suffering from amalarial infection. In particular, the compositions of the presentinvention may be administered to a patient suffering from a malarialinfection to treat symptoms associated with that infection. Moreparticularly, these compositions may be administered to the patient toprevent or reduce erythrocyte sequestration and the resultingmicrovascular occlusion associated with malarial, and more specifically,P. falciparum, infections.

Although the polypeptides, nucleic acids and antibodies of the presentinvention may be administered alone, for therapeutic and prophylacticapplications, these elements will generally be administered as part of apharmaceutical composition, e.g., in combination with a pharmaceuticallyacceptable carrier. Typically, a single composition may be used in boththerapeutic and prophylactic applications. Pharmaceutical formulationssuitable for use in the present invention are generally described inRemington's Pharmaceutical Sciences, Mack Publishing Co., 17th ed.(1985).

The pharmaceutical compositions of the present invention are intendedfor parenteral, topical, oral, or local administration. Where thepharmaceutical compositions are administered parenterally, the inventionprovides pharmaceutical compositions that comprise a solution of theagents described above, e.g., polypeptides of the invention, dissolvedor suspended in a pharmaceutically acceptable carrier, preferably anaqueous carrier. A variety of aqueous carriers may be used, e.g., water,buffered water, saline glycine, and the like. These compositions may besterilized by conventional, well known methods, e.g., sterilefiltration. The resulting aqueous solutions may be packaged for use asis, or lyophilized for combination with a sterile solution prior toadministration. The compositions may contain pharmaceutically acceptableauxiliary substances as required to approximate physiologicalconditions, such as pH adjusting and buffering agents, tonicityadjusting agents, wetting agents, and the like, for example sodiumacetate, sodium lactate, sodium chloride, potassium chloride, calciumchloride, sorbitan monolaurate, triethanolamine oleate, etc.

For solid compositions, conventional nontoxic solid carriers may be usedwhich include, for example, pharmaceutical grades of mannitol, lactosestarch, magnesium stearate, sodium saccharin, talcum, cellulose,glucose, sucrose, magnesium carbonate, and the like. For oraladministration, a pharmaceutically acceptable nontoxic composition maybe formed by incorporating any of the normally employed excipients, suchas the previously listed carriers, and generally, 10-95% of activeingredient, and more preferably 25-75% active ingredient. In addition,for oral administration of peptide based compounds, the pharmaceuticalcompositions may include the active ingredient as part of a matrix toprevent proteolytic degradation of the active ingredient by digestiveprocess, e.g., by providing the pharmaceutical composition within aliposomal composition, according to methods well known in the art. See,e.g., Remington's Pharmaceutical Sciences, Mack Publishing Co., 17th Ed.(1985).

For aerosol administration, the polypeptides are generally supplied infinely divided form along with a surfactant or propellant. Preferably,the surfactant will be soluble in the propellant. Representative of suchagents are the esters or partial esters of fatty acids containing from 6to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic,stearic, linoleic, linolenic, olesteric and oleic acids, with analiphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, suchas mixed or natural glycerides may be employed. A carrier can also beincluded, as desired, as with, e.g., lecithin for intranasal delivery.The above described compositions are suitable for a singleadministration or a series of administrations. When given as a series,e.g., as a vaccine booster, the inoculations subsequent to the initialadministration are given to boost the immune response, and are typicallyreferred to as booster inoculations.

The amount of the above compositions to be administered to the patientwill vary depending upon what is to be administered to the patient, thestate of the patient, the manner of administration, and the particularapplication, e.g., therapeutic or prophylactic. In therapeuticapplications, the compositions are administered to the patient alreadysuffering from a malarial infection, in an amount sufficient to inhibitthe spread of the parasite through the erythrocytes, and thereby cure orat least partially arrest the symptoms of the disease and its associatedcomplications.

An amount adequate to accomplish this is termed “a therapeuticallyeffective amount.” Amounts effective for this use will depend upon theseverity of the disease and the weight and general state of the patient,but will generally be in the range of from about 1 mg to about 5 g ofactive agent per day, preferably from about 50 mg per day to about 500mg per day, and more preferably, from about 50 mg to about 100 mg perday, for a 70 kg patient.

For prophylactic applications, immunogenically effective amounts willalso depend upon the composition, the manner of administration and theweight and general state of the patient, as well as the judgment of theprescribing physician. For the peptide, peptide analog and antibodybased pharmaceutical compositions, the general range for the initialimmunization (for either prophylactic or therapeutic applications) willbe from about 100 μg to about 1 g of polypeptide for a 70 kg patient,followed by boosting dosages of from about 1 μg to about 1 gm ofpolypeptide pursuant to a boosting regimen over weeks to months,depending upon the patient's response and condition, e.g., by measuringthe level of parasite or antibodies in the patient's blood. For nucleicacids, typically from about 30 to about 100 μg of nucleic acid isinjected into a 70 kg patient, more typically, about 50 to 150 μg ofnucleic acid is injected, followed by boosting treatments asappropriate.

The present invention is further illustrated by the following examples.These examples are merely to illustrate aspects of the present inventionand are not intended as limitations of this invention.

2.11. Directed Evolution Methods

In one aspect the invention described herein is directed to the use ofrepeated cycles of reductive reassortment, recombination and selectionwhich allow for the directed molecular evolution of highly complexlinear sequences, such as DNA, RNA or proteins thorough recombination.

In vivo shuffling of molecules can be performed utilizing the naturalproperty of cells to recombine multimers. While recombination in vivohas provided the major natural route to molecular diversity, geneticrecombination remains a relatively complex process that involves 1) therecognition of homologies; 2) strand cleavage, strand invasion, andmetabolic steps leading to the production of recombinant chiasma; andfinally 3) the resolution of chiasma into discrete recombined molecules.The formation of the chiasma requires the recognition of homologoussequences.

In a preferred embodiment, the invention relates to a method forproducing a hybrid polynucleotide from at least a first polynucleotideand a second polynucleotide. The present invention can be used toproduce a hybrid polynucleotide by introducing at least a firstpolynucleotide and a second polynucleotide which share at least oneregion of partial sequence homology into a suitable host cell. Theregions of partial sequence homology promote processes which result insequence reorganization producing a hybrid polynucleotide. The term“hybrid polynucleotide”, as used herein, is any nucleotide sequencewhich results from the method of the present invention and containssequence from at least two original polynucleotide sequences. Suchhybrid polynucleotides can result from intermolecular recombinationevents which promote sequence integration between DNA molecules. Inaddition, such hybrid polynucleotides can result from intramolecularreductive reassortment processes which utilize repeated sequences toalter a nucleotide sequence within a DNA molecule.

The invention provides a means for generating hybrid polynucleotideswhich may encode biologically active hybrid polypeptides. In one aspect,the original polynucleotides encode biologically active polypeptides.The method of the invention produces new hybrid polypeptides byutilizing cellular processes which integrate the sequence of theoriginal polynucleotides such that the resulting hybrid polynucleotideencodes a polypeptide demonstrating activities derived from the originalbiologically active polypeptides. For example, the originalpolynucleotides may encode a particular enzyme from differentmicroorganisms. An enzyme encoded by a first polynucleotide from oneorganism may, for example, function effectively under a particularenvironmental condition, e.g. high salinity. An enzyme encoded by asecond polynucleotide from a different organism may function effectivelyunder a different environmental condition, such as extremely hightemperatures. A hybrid polynucleotide containing sequences from thefirst and second original polynucleotides may encode an enzyme whichexhibits characteristics of both enzymes encoded by the originalpolynucleotides. Thus, the enzyme encoded by the hybrid polynucleotidemay function effectively under environmental conditions shared by eachof the enzymes encoded by the first and second polynucleotides, e.g.,high salinity and extreme temperatures.

Enzymes encoded by the original polynucleotides of the inventioninclude, but are not limited to; oxidoreductases, transferases,hydrolases, lyases, isomerases and ligases. A hybrid polypeptideresulting from the method of the invention may exhibit specializedenzyme activity not displayed in the original enzymes. For example,following recombination and/or reductive reassortment of polynucleotidesencoding hydrolase activities, the resulting hybrid polypeptide encodedby a hybrid polynucleotide can be screened for specialized hydrolaseactivities obtained from each of the original enzymes, i.e. the type ofbond on which the hydrolase acts and the temperature at which thehydrolase functions. Thus, for example, the hydrolase may be screened toascertain those chemical functionalities which distinguish the hybridhydrolase from the original hydrolyases, such as: (a) amide (peptidebonds), i.e. proteases; (b) ester bonds, i.e. esterases and lipases; (c)acetals, i.e., glycosidases and, for example, the temperature, pH orsalt concentration at which the hybrid polypeptide functions.

Sources of the original polynucleotides may be isolated from individualorganisms (“isolates”), collections of organisms that have been grown indefined media (“enrichment cultures”), or, most preferably, uncultivatedorganisms (“environmental samples”). The use of a culture-independentapproach to derive polynucleotides encoding novel bioactivities fromenvironmental samples is most preferable since it allows one to accessuntapped resources of biodiversity.

“Environmental libraries” are generated from environmental samples andrepresent the collective genomes of naturally occurring organismsarchived in cloning vectors that can be propagated in suitableprokaryotic hosts. Because the cloned DNA is initially extracteddirectly from environmental samples, the libraries are not limited tothe small fraction of prokaryotes that can be grown in pure culture.Additionally, a normalization of the environmental DNA present in thesesamples could allow more equal representation of the DNA from all of thespecies present in the original sample. This can dramatically increasethe efficiency of finding interesting genes from minor constituents ofthe sample which may be under-represented by several orders of magnitudecompared to the dominant species.

For example, gene libraries generated from one or more uncultivatedmicroorganisms are screened for an activity of interest. Potentialpathways encoding bioactive molecules of interest are first captured inprokaryotic cells in the form of gene expression libraries.Polynucleotides encoding activities of interest are isolated from suchlibraries and introduced into a host cell. The host cell is grown underconditions which promote recombination and/or reductive reassortmentcreating potentially active biomolecules with novel or enhancedactivities.

The microorganisms from which the polynucleotide may be prepared includeprokaryotic microorganisms, such as Eubacteria and Archaebacteria, andlower eukaryotic microorganisms such as fungi, some algae and protozoa.Polynucleotides may be isolated from environmental samples in which casethe nucleic acid may be recovered without culturing of an organism orrecovered from one or more cultured organisms. In one aspect, suchmicroorganisms may be extremophiles, such as hyperthermophiles,psychrophiles, psychrotrophs, halophiles, barophiles and acidophiles.Polynucleotides encoding enzymes isolated from extremophilicmicroorganisms are particularly preferred. Such enzymes may function attemperatures above 100° C. in terrestrial hot springs and deep seathermal vents, at temperatures below 0° C. in arctic waters, in thesaturated salt environment of the Dead Sea, at pH values around 0 incoal deposits and geothermal sulfur-rich springs, or at pH valuesgreater than 11 in sewage sludge. For example, several esterases andlipases cloned and expressed from extremophilic organisms show highactivity throughout a wide range of temperatures and pHs.

Polynucleotides selected and isolated as hereinabove described areintroduced into a suitable host cell. A suitable host cell is any cellwhich is capable of promoting recombination and/or reductivereassortment. The selected polynucleotides are preferably already in avector which includes appropriate control sequences. The host cell canbe a higher eukaryotic cell, such as a mammalian cell, or a lowereukaryotic cell, such as a yeast cell, or preferably, the host cell canbe a prokaryotic cell, such as a bacterial cell. Introduction of theconstruct into the host cell can be effected by calcium phosphatetransfection, DEAE-Dextran mediated transfection, or electroporation(Davis et al, 1986).

As representative examples of appropriate hosts, there may be mentioned:bacterial cells, such as E. coli, Streptomyces, Salmonella typhimurium;fungal cells, such as yeast; insect cells such as Drosophila S2 andSpodoptera SJ9; animal cells such as CHO, COS or Bowes melanoma;adenoviruses; and plant cells. The selection of an appropriate host isdeemed to be within the scope of those skilled in the art from theteachings herein.

With particular references to various mammalian cell culture systemsthat can be employed to express recombinant protein, examples ofmammalian expression systems include the COS-7 lines of monkey kidneyfibroblasts, described in “SV40-transformed simian cells support thereplication of early SV40 mutants” (Gluzman, 1981), and other cell linescapable of expressing a compatible vector, for example, the C127, 3T3,CHO, HeLa and BHK cell lines. Mammalian expression vectors will comprisean origin of replication, a suitable promoter and enhancer, and also anynecessary ribosome binding sites, polyadenylation site, splice donor andacceptor sites, transcriptional termination sequences, and 5′ flankingnontranscribed sequences. DNA sequences derived from the SV40 splice,and polyadenylation sites may be used to provide the requirednontranscribed genetic elements.

Host cells containing the polynucleotides of interest can be cultured inconventional nutrient media modified as appropriate for activatingpromoters, selecting transformants or amplifying genes. The cultureconditions, such as temperature, pH and the like, are those previouslyused with the host cell selected for expression, and will be apparent tothe ordinarily skilled artisan. The clones which are identified ashaving the specified enzyme activity may then be sequenced to identifythe polynucleotide sequence encoding an enzyme having the enhancedactivity.

In another aspect, it is envisioned the method of the present inventioncan be used to generate novel polynucleotides encoding biochemicalpathways from one or more operons or gene clusters or portions thereof.For example, bacteria and many eukaryotes have a coordinated mechanismfor regulating genes whose products are involved in related processes.The genes are clustered, in structures referred to as “gene clusters,”on a single chromosome and are transcribed together under the control ofa single regulatory sequence, including a single promoter whichinitiates transcription of the entire cluster. Thus, a gene cluster is agroup of adjacent genes that are either identical or related, usually asto their function. An example of a biochemical pathway encoded by geneclusters are polyketides. Polyketides are molecules which are anextremely rich source of bioactivities, including antibiotics (such astetracyclines and erythromycin), anti-cancer agents (daunomycin),immunosuppressants (FK506 and rapamycin), and veterinary products(monensin). Many polyketides (produced by polyketide synthases) arevaluable as therapeutic agents. Polyketide synthases are multifunctionalenzymes that catalyze the biosynthesis of an enormous variety of carbonchains differing in length and patterns of functionality andcyclization. Polyketide synthase genes fall into gene clusters and atleast one type (designated type I) of polyketide synthases have largesize genes and enzymes, complicating genetic manipulation and in vitrostudies of these genes/proteins.

The ability to select and combine desired components from a library ofpolyketides, or fragments thereof, and postpolyketide biosynthesis genesfor generation of novel polyketides for study is appealing. The methodof the present invention makes it possible to facilitate the productionof novel polyketide synthases through intermolecular recombination.

Preferably, gene cluster DNA can be isolated from different organismsand ligated into vectors, particularly vectors containing expressionregulatory sequences which can control and regulate the production of adetectable protein or protein-related array activity from the ligatedgene clusters. Use of vectors which have an exceptionally large capacityfor exogenous DNA introduction are particularly appropriate for use withsuch gene clusters and are described by way of example herein to includethe f-factor (or fertility factor) of E. coli. This f-factor of E. coliis a plasmid which affect high-frequency transfer of itself duringconjugation and is ideal to achieve and stably propagate large DNAfragments, such as gene clusters from mixed microbial samples. Onceligated into an appropriate vector, two or more vectors containingdifferent polyketide synthase gene clusters can be introduced into asuitable host cell. Regions of partial sequence homology shared by thegene clusters will promote processes which result in sequencereorganization resulting in a hybrid gene cluster. The novel hybrid genecluster can then be screened for enhanced activities not found in theoriginal gene clusters.

Therefore, in a preferred embodiment, the present invention relates to amethod for producing a biologically active hybrid polypeptide andscreening such a polypeptide for enhanced activity by:

-   -   1) introducing at least a first polynucleotide in operable        linkage and a second polynucleotide in operable linkage, said at        least first polynucleotide and second polynucleotide sharing at        least one region of partial sequence homology, into a suitable        host cell;    -   2) growing the host cell under conditions which promote sequence        reorganization resulting in a hybrid polynucleotide in operable        linkage;    -   3) expressing a hybrid polypeptide encoded by the hybrid        polynucleotide;    -   4) screening the hybrid polypeptide under conditions which        promote identification of enhanced biological activity; and    -   5) isolating the a polynucleotide encoding the hybrid        polypeptide.

Methods for screening for various enzyme activities are known to thoseof skill in the art and discussed throughout the present specification.Such methods may be employed when isolating the polypeptides andpolynucleotides of the present invention.

As representative examples of expression vectors which may be used theremay be mentioned viral particles, baculovirus, phage, plasmids,phagemids, cosmids, fosmids, bacterial artificial chromosomes, viral DNA(e.g. vaccinia, adenovirus, foul pox virus, pseudorabies and derivativesof SV40), P1-based artificial chromosomes, yeast plasmids, yeastartificial chromosomes, and any other vectors specific for specifichosts of interest (such as bacillus, aspergillus and yeast). Thus, forexample, the DNA may be included in any one of a variety of expressionvectors for expressing a polypeptide. Such vectors include chromosomal,nonchromosomal and synthetic DNA sequences. Large numbers of suitablevectors are known to those of skill in the art, and are commerciallyavailable. The following vectors are provided by way of example;Bacterial: pQE vectors (Qiagen), pBluescript plasmids, pNH vectors,(lambda-ZAP vectors (Stratagene); ptrc99a, pKK223-3, pDR540, pRIT2T(Pharmacia); Eukaryotic: pXT1, pSG5 (Stratagene), pSVK3, pBPV, PMSG,pSVLSV40 (Pharmacia). However, any other plasmid or other vector may beused as long as they are replicable and viable in the host. Low copynumber or high copy number vectors may be employed with the presentinvention.

A preferred type of vector for use in the present invention contains anf-factor origin replication. The f-factor (or fertility factor) in E.coli is a plasmid which effects high frequency transfer of itself duringconjugation and less frequent transfer of the bacterial chromosomeitself. A particularly preferred embodiment is to use cloning vectors,referred to as “fosmids” or bacterial artificial chromosome (BAC)vectors. These are derived from E. coli f-factor which is able to stablyintegrate large segments of genomic DNA. When integrated with DNA from amixed uncultured environmental sample, this makes it possible to achievelarge genomic fragments in the form of a stable “environmental DNAlibrary.”

Another preferred type of vector for use in the present invention is acosmid vector. Cosmid vectors were originally designed to clone andpropagate large segments of genomic DNA. Cloning into cosmid vectors isdescribed in detail in “Molecular Cloning: A laboratory Manual”(Sambrook et al, 1989).

The DNA sequence in the expression vector is operatively linked to anappropriate expression control sequence(s) (promoter) to direct RNAsynthesis. Particular named bacterial promoters include lacI, lacZ, T3,T7, gpt, lambda P_(R), P_(L) and trp. Eukaryotic promoters include CMVimmediate early, HSV thymidine kinase, early and late SV40, LTRs fromretrovirus, and mouse metallothionein-I. Selection of the appropriatevector and promoter is well within the level of ordinary skill in theart. The expression vector also contains a ribosome binding site fortranslation initiation and a transcription terminator. The vector mayalso include appropriate sequences for amplifying expression. Promoterregions can be selected from any desired gene using CAT (chloramphenicoltransferase) vectors or other vectors with selectable markers.

In addition, the expression vectors preferably contain one or moreselectable marker genes to provide a phenotypic trait for selection oftransformed host cells such as dihydrofolate reductase or neomycinresistance for eukaryotic cell culture, or such as tetracycline orampicillin resistance in E. coli.

Generally, recombinant expression vectors will include origins ofreplication and selectable markers permitting transformation of the hostcell, e.g., the ampicillin resistance gene of E. coli and S. cerevisiaeTRP1 gene, and a promoter derived from a highly-expressed gene to directtranscription of a downstream structural sequence. Such promoters can bederived from operons encoding glycolytic enzymes such as3-phosphoglycerate kinase (PGK), α-factor, acid phosphatase, or heatshock proteins, among others. The heterologous structural sequence isassembled in appropriate phase with translation initiation andtermination sequences, and preferably, a leader sequence capable ofdirecting secretion of translated protein into the periplasmic space orextracellular medium.

The cloning strategy permits expression via both vector driven andendogenous promoters; vector promotion may be important with expressionof genes whose endogenous promoter will not function in E. coli.

The DNA isolated or derived from microorganisms can preferably beinserted into a vector or a plasmid prior to probing for selected DNA.Such vectors or plasmids are preferably those containing expressionregulatory sequences, including promoters, enhancers and the like. Suchpolynucleotides can be part of a vector and/or a composition and stillbe isolated, in that such vector or composition is not part of itsnatural environment. Particularly preferred phage or plasmid and methodsfor introduction and packaging into them are described in detail in theprotocol set forth herein.

The selection of the cloning vector depends upon the approach taken, forexample, the vector can be any cloning vector with an adequate capacityto multiply repeated copies of a sequence, or multiple sequences thatcan be successfully transformed and selected in a host cell. One exampleof such a vector is described in “Polycos vectors: a system forpackaging filamentous phage and phagemid vectors using lambda phagepackaging extracts” (Alting-Mecs and Short, 1993).Propagation/maintenance can be by an antibiotic resistance carried bythe cloning vector. After a period of growth, the naturally abbreviatedmolecules are recovered and identified by size fractionation on a gel orcolumn, or amplified directly. The cloning vector utilized may contain aselectable gene that is disrupted by the insertion of the lengthyconstruct. As reductive reassortment progresses, the number of repeatedunits is reduced and the interrupted gene is again expressed and henceselection for the processed construct can be applied. The vector may bean expression/selection vector which will allow for the selection of anexpressed product possessing desirable biologically properties. Theinsert may be positioned downstream of a functional promotor and thedesirable property screened by appropriate means.

In vivo reassortment is focused on “inter-molecular” processescollectively referred to as “recombination” which in bacteria, isgenerally viewed as a “RecA-dependent” phenomenon. The present inventioncan rely on recombination processes of a host cell to recombine andre-assort sequences, or the cells' ability to mediate reductiveprocesses to decrease the complexity of quasi-repeated sequences in thecell by deletion. This process of “reductive reassortment” occurs by an“intra-molecular”, RecA-independent process.

Therefore, in another aspect of the present invention, novelpolynucleotides can be generated by the process of reductivereassortment. The method involves the generation of constructscontaining consecutive sequences (original encoding sequences), theirinsertion into an appropriate vector, and their subsequent introductioninto an appropriate host cell. The reassortment of the individualmolecular identities occurs by combinatorial processes between theconsecutive sequences in the construct possessing regions of homology,or between quasi-repeated units. The reassortment process recombinesand/or reduces the complexity and extent of the repeated sequences, andresults in the production of novel molecular species. Various treatmentsmay be applied to enhance the rate of reassortment. These could includetreatment with ultra-violet light, or DNA damaging chemicals, and/or theuse of host cell lines displaying enhanced levels of “geneticinstability”. Thus the reassortment process may involve homologousrecombination or the natural property of quasi-repeated sequences todirect their own evolution.

Repeated or “quasi-repeated” sequences play a role in geneticinstability. In the present invention, “quasi-repeats” are repeats thatare not restricted to their original unit structure. Quasi-repeatedunits can be presented as an array of sequences in a construct;consecutive units of similar sequences. Once ligated, the junctionsbetween the consecutive sequences become essentially invisible and thequasi-repetitive nature of the resulting construct is now continuous atthe molecular level. The deletion process the cell performs to reducethe complexity of the resulting construct operates between thequasi-repeated sequences. The quasi-repeated units provide a practicallylimitless repertoire of templates upon which slippage events can occur.The constructs containing the quasi-repeats thus effectively providesufficient molecular elasticity that deletion (and potentiallyinsertion) events can occur virtually anywhere within thequasi-repetitive units.

When the quasi-repeated sequences are all ligated in the sameorientation, for instance head to tail or vice versa, the cell cannotdistinguish individual units. Consequently, the reductive process canoccur throughout the sequences. In contrast, when for example, the unitsare presented head to head, rather than head to tail, the inversiondelineates the endpoints of the adjacent unit so that deletion formationwill favor the loss of discrete units. Thus, it is preferable with thepresent method that the sequences are in the same orientation. Randomorientation of quasi-repeated sequences will result in the loss ofreassortment efficiency, while consistent orientation of the sequenceswill offer the highest efficiency. However, while having fewer of thecontiguous sequences in the same orientation decreases the efficiency,it may still provide sufficient elasticity for the effective recovery ofnovel molecules. Constructs can be made with the quasi-repeatedsequences in the same orientation to allow higher efficiency.

Sequences can be assembled in a head to tail orientation using any of avariety of methods, including the following:

-   -   a) Primers that include a poly-A head and poly-T tail which when        made single-stranded would provide orientation can be utilized.        This is accomplished by having the first few bases of the        primers made from RNA and hence easily removed RNAseH.    -   b) Primers that include unique restriction cleavage sites can be        utilized. Multiple sites, a battery of unique sequences, and        repeated synthesis and ligation steps would be required.    -   c) The inner few bases of the primer could be thiolated and an        exonuclease used to produce properly tailed molecules.

The recovery of the re-assorted sequences relies on the identificationof cloning vectors with a reduced RI. The re-assorted encoding sequencescan then be recovered by amplification. The products are re-cloned andexpressed. The recovery of cloning vectors with reduced RI can beeffected by:

-   1) The use of vectors only stably maintained when the construct is    reduced in complexity.-   2) The physical recovery of shortened vectors by physical    procedures. In this case, the cloning vector would be recovered    using standard plasmid isolation procedures and size fractionated on    either an agarose gel, or column with a low molecular weight cut off    utilizing standard procedures.-   3) The recovery of vectors containing interrupted genes which can be    selected when insert size decreases.-   4) The use of direct selection techniques with an expression vector    and the appropriate selection.

Encoding sequences (for example, genes) from related organisms maydemonstrate a high degree of homology and encode quite diverse proteinproducts. These types of sequences are particularly useful in thepresent invention as quasi-repeats. However, while the examplesillustrated below demonstrate the reassortment of nearly identicaloriginal encoding sequences (quasi-repeats), this process is not limitedto such nearly identical repeats.

The following example demonstrates the method of the invention. Encodingnucleic acid sequences (quasi-repeats) derived from three (3) uniquespecies are depicted. Each sequence encodes a protein with a distinctset of properties. Each of the sequences differs by a single or a fewbase pairs at a unique position in the sequence which are designated“A”, “B” and “C”. The quasi-repeated sequences are separately orcollectively amplified and ligated into random assemblies such that allpossible permutations and combinations are available in the populationof ligated molecules. The number of quasi-repeat units can be controlledby the assembly conditions. The average number of quasi-repeated unitsin a construct is defined as the repetitive index (RI).

Once formed, the constructs may, or may not be size fractionated on anagarose gel according to published protocols, inserted into a cloningvector, and transfected into an appropriate host cell. The cells arethen propagated and “reductive reassortment” is effected. The rate ofthe reductive reassortment process may be stimulated by the introductionof DNA damage if desired. Whether the reduction in RI is mediated bydeletion formation between repeated sequences by an “intra-molecular”mechanism, or mediated by recombination-like events through“inter-molecular” mechanisms is immaterial. The end result is areassortment of the molecules into all possible combinations.

Optionally, the method comprises the additional step of screening thelibrary members of the shuffled pool to identify individual shuffledlibrary members having the ability to bind or otherwise interact (e.g.,such as catalytic antibodies) with a predetermined macromolecule, suchas for example a proteinaceous receptor, peptide oligosaccharide, viron,or other predetermined compound or structure.

The displayed polypeptides, antibodies, peptidomimetic antibodies, andvariable region sequences that are identified from such libraries can beused for therapeutic, diagnostic, research and related purposes (e.g.,catalysts, solutes for increasing osmolarity of an aqueous solution, andthe like), and/or can be subjected to one or more additional cycles ofshuffling and/or affinity selection. The method can be modified suchthat the step of selecting for a phenotypic characteristic can be otherthan of binding affinity for a predetermined molecule (e.g., forcatalytic activity, stability oxidation resistance, drug resistance, ordetectable phenotype conferred upon a host cell).

The present invention provides a method for generating libraries ofdisplayed antibodies suitable for affinity interactions screening. Themethod comprises (1) obtaining first a plurality of selected librarymembers comprising a displayed antibody and an associated polynucleotideencoding said displayed antibody, and obtaining said associatedpolynucleotide encoding for said displayed antibody and obtaining saidassociated polynucleotides or copies thereof, wherein said associatedpolynucleotides comprise a region of substantially identical variableregion framework sequence, and (2) introducing said polynucleotides intoa suitable host cell and growing the cells under conditions whichpromote recombination and reductive reassortment resulting in shuffledpolynucleotides. CDR combinations comprised by the shuffled pool are notpresent in the first plurality of selected library members, saidshuffled pool composing a library of displayed antibodies comprising CDRpermutations and suitable for affinity interaction screening.Optionally, the shuffled pool is subjected to affinity screening toselect shuffled library members which bind to a predetermined epitope(antigen) and thereby selecting a plurality of selected shuffled librarymembers. Further, the plurality of selectively shuffled library memberscan be shuffled and screened iteratively, from 1 to about 1000 cycles oras desired until library members having a desired binding affinity areobtained.

In another aspect of the invention, it is envisioned that prior to orduring recombination or reassortment, polynucleotides generated by themethod of the present invention can be subjected to agents or processeswhich promote the introduction of mutations into the originalpolynucleotides. The introduction of such mutations would increase thediversity of resulting hybrid polynucleotides and polypeptides encodedtherefrom. The agents or processes which promote mutagenesis caninclude, but are not limited to: (+)-CC-1065, or a synthetic analog suchas (+)-CC-1065-(N3-Adenine, see Sun and Hurley, 1992); an N-acetylatedor deacetylated 4′-fluoro-4-aminobiphenyl adduct capable of inhibitingDNA synthesis (see, for example, van de Poll et al, 1992); or aN-acetylated or deacetylated 4-aminobiphenyl adduct capable ofinhibiting DNA synthesis (see also, van de Poll et al, 1992, pp.751-758); trivalent chromium, a trivalent chromium salt, a polycyclicaromatic hydrocarbon (“PAH”) DNA adduct capable of inhibiting DNAreplication, such as 7-bromomethyl-benz[a]anthracene (“BMA”),tris(2,3-dibromopropyl)phosphate (“Tris-BP”),1,2-dibromo-3-chloropropane (“DBCP”), 2-bromoacrolein (2BA),benzo[a]pyrene-7,8-dihydrodiol-9-10-epoxide (“BPDE”), a platinum(II)halogen salt, N-hydroxy-2-amino-3-methylimidazo[4,5-j]-quinoline(“N-hydroxy-IQ”), andN-hydroxy-2-amino-1-methyl-6-phenylimidazo[4,5-j]-pyridine(“N-hydroxy-PhIP”). Especially preferred “means for slowing or haltingPCR amplification consist of UV light (+)-CC-1065 and(+)-CC-1065-(N3-Adenine). Particularly encompassed means are DNA adductsor polynucleotides comprising the DNA adducts from the polynucleotidesor polynucleotides pool, which can be released or removed by a processincluding heating the solution comprising the polynucleotides prior tofurther processing.

In another aspect the present invention is directed to a method ofproducing recombinant proteins having biological activity by treating asample comprising double-stranded template polynucleotides encoding awild-type protein under conditions according to the present inventionwhich provide for the production of hybrid or re-assortedpolynucleotides.

The invention also provides the use of polynucleotide shuffling toshuffle a population of viral genes (e.g., capsid proteins, spikeglycoproteins, polymerases, and proteases) or viral genomes (e.g.,paramyxoviridae, orthomyxoviridae, herpesviruses, retroviruses,reoviruses and rhinoviruses). In an embodiment, the invention provides amethod for shuffling sequences encoding all or portions of immunogenicviral proteins to generate novel combinations of epitopes as well asnovel epitopes created by recombination; such shuffled viral proteinsmay comprise epitopes or combinations of epitopes as well as novelepitopes created by recombination; such shuffled viral proteins maycomprise epitopes or combinations of epitopes which are likely to arisein the natural environment as a consequence of viral evolution; (e.g.,such as recombination of influenza virus strains).

The invention also provides a method suitable for shufflingpolynucleotide sequences for generating gene therapy vectors andreplication-defective gene therapy constructs, such as may be used forhuman gene therapy, including but not limited to vaccination vectors forDNA-based vaccination, as well as anti-neoplastic gene therapy and othergeneral therapy formats.

In the polypeptide notation used herein, the left-hand direction is theamino terminal direction and the right-hand direction is thecarboxy-terminal direction, in accordance with standard usage andconvention. Similarly, unless specified otherwise, the left-hand end ofsingle-stranded polynucleotide sequences is the 5′ end; the left-handdirection of double-stranded polynucleotide sequences is referred to asthe 5′ direction. The direction of 5′ to 3′ addition of nascent RNAtranscripts is referred to as the transcription direction; sequenceregions on the DNA strand having the same sequence as the RNA and whichare 5′ to the 5′ end of the RNA transcript are referred to as “upstreamsequences”; sequence regions on the DNA strand having the same sequenceas the RNA and which are 3′ to the 3′ end of the coding RNA transcriptare referred to as “downstream sequences”.

2.11.1. Saturation Mutagenesis

In one aspect, this invention provides for the use of proprietary codonprimers (containing a degenerate N,N,G/T sequence) to introduce pointmutations into a polynucleotide, so as to generate a set of progenypolypeptides in which a full range of single amino acid substitutions isrepresented at each amino acid position. The oligos used are comprisedcontiguously of a first homologous sequence, a degenerate N,N,G/Tsequence, and preferably but not necessarily a second homologoussequence. The downstream progeny translational products from the use ofsuch oligos include all possible amino acid changes at each amino acidsite along the polypeptide, because the degeneracy of the N,N,G/Tsequence includes codons for all 20 amino acids.

In one aspect, one such degenerate oligo (comprised of one degenerateN,N,G/T cassette) is used for subjecting each original codon in aparental polynucleotide template to a full range of codon substitutions.In another aspect, at least two degenerate N,N,G/T cassettes areused—either in the same oligo or not, for subjecting at least twooriginal codons in a parental polynucleotide template to a full range ofcodon substitutions. Thus, more than one N,N,G/T sequence can becontained in one oligo to introduce amino acid mutations at more thanone site. This plurality of N,N,G/T sequences can be directlycontiguous, or separated by one or more additional nucleotidesequence(s). In another aspect, oligos serviceable for introducingadditions and deletions can be used either alone or in combination withthe codons containing an N,N,G/T sequence, to introduce any combinationor permutation of amino acid additions, deletions, and/or substitutions.

In a particular exemplification, it is possible to simultaneouslymutagenize two or more contiguous amino acid positions using an oligothat contains contiguous N,N,G/T triplets, i.e. a degenerate(N,N,G/T)_(n) sequence.

In another aspect, the present invention provides for the use ofdegenerate cassettes having less degeneracy than the N,N,G/T sequence.For example, it may be desirable in some instances to use (e.g. in anoligo) a degenerate triplet sequence comprised of only one N, where saidN can be in the first second or third position of the triplet. Any otherbases including any combinations and permutations thereof can be used inthe remaining two positions of the triplet. Alternatively, it may bedesirable in some instances to use (e.g. in an oligo) a degenerate N,N,Ntriplet sequence, or an N,N, G/C triplet sequence.

It is appreciated, however, that the use of a degenerate triplet (suchas N,N,G/T or an N,N, G/C triplet sequence) as disclosed in the instantinvention is advantageous for several reasons. In one aspect, thisinvention provides a means to systematically and fairly easily generatethe substitution of the full range of possible amino acids (for a totalof 20 amino acids) into each and every amino acid position in apolypeptide. Thus, for a 100 amino acid polypeptide, the instantinvention provides a way to systematically and fairly easily generate2000 distinct species (i.e. 20 possible amino acids per position×100amino acid positions). It is appreciated that there is provided, throughthe use of an oligo containing a degenerate N,N,G/T or an N,N, G/Ctriplet sequence, 32 individual sequences that code for 20 possibleamino acids. Thus, in a reaction vessel in which a parentalpolynucleotide sequence is subjected to saturation mutagenesis using onesuch oligo, there are generated 32 distinct progeny polynucleotidesencoding 20 distinct polypeptides. In contrast, the use of anon-degenerate oligo in site-directed mutagenesis leads to only oneprogeny polypeptide product per reaction vessel.

This invention also provides for the use of nondegenerate oligos, whichcan optionally be used in combination with degenerate primers disclosed.It is appreciated that in some situations, it is advantageous to usenondegenerate oligos to generate specific point mutations in a workingpolynucleotide. This provides a means to generate specific silent pointmutations, point mutations leading to corresponding amino acid changes,and point mutations that cause the generation of stop codons and thecorresponding expression of polypeptide fragments.

Thus, in a preferred embodiment of this invention, each saturationmutagenesis reaction vessel contains polynucleotides encoding at least20 progeny polypeptide molecules such that all 20 amino acids arerepresented at the one specific amino acid position corresponding to thecodon position mutagenized in the parental polynucleotide. The 32-folddegenerate progeny polypeptides generated from each saturationmutagenesis reaction vessel can be subjected to clonal amplification(e.g. cloned into a suitable E. coli host using an expression vector)and subjected to expression screening. When an individual progenypolypeptide is identified by screening to display a favorable change inproperty (when compared to the parental polypeptide), it can besequenced to identify the correspondingly favorable amino acidsubstitution contained therein.

It is appreciated that upon mutagenizing each and every amino acidposition in a parental polypeptide using saturation mutagenesis asdisclosed herein, favorable amino acid changes may be identified at morethan one amino acid position. One or more new progeny molecules can begenerated that contain a combination of all or part of these favorableamino acid substitutions. For example, if 2 specific favorable aminoacid changes are identified in each of 3 amino acid positions in apolypeptide, the permutations include 3 possibilities at each position(no change from the original amino acid, and each of two favorablechanges) and 3 positions. Thus, there are 3×3×3 or 27 totalpossibilities, including 7 that were previously examined—6 single pointmutations (i.e. 2 at each of three positions) and no change at anyposition.

In yet another aspect, site-saturation mutagenesis can be used togetherwith shuffling, chimerization, recombination and other mutagenizingprocesses, along with screening. This invention provides for the use ofany mutagenizing process(es), including saturation mutagenesis, in aniterative manner. In one exemplification, the iterative use of anymutagenizing process(es) is used in combination with screening.

Thus, in a non-limiting exemplification, this invention provides for theuse of saturation mutagenesis in combination with additionalmutagenization processes, such as process where two or more relatedpolynucleotides are introduced into a suitable host cell such that ahybrid polynucleotide is generated by recombination and reductivereassortment.

In addition to performing mutagenesis along the entire sequence of agene, the instant invention provides that mutagenesis can be use toreplace each of any number of bases in a polynucleotide sequence,wherein the number of bases to be mutagenized is preferably everyinteger from 15 to 100,000. Thus, instead of mutagenizing every positionalong a molecule, one can subject every a discrete number of bases(preferably a subset totaling from 15 to 100,000) to mutagenesis.Preferably, a separate nucleotide is used for mutagenizing each positionor group of positions along a polynucleotide sequence. A group of 3positions to be mutagenized may be a codon. The mutations are preferablyintroduced using a mutagenic primer, containing a heterologous cassette,also referred to as a mutagenic cassette. Preferred cassettes can havefrom 1 to 500 bases. Each nucleotide position in such heterologouscassettes be N, A, C, G, T, A/C, A/G, A/T, C/G, C/T, G/T, C/G/T, A/G/T,A/C/T, A/C/G, or E, where E is any base that is not A, C, G, or T (E canbe referred to as a designer oligo). The tables below show exemplarytri-nucleotide cassettes (there are over 3000 possibilities in additionto N,N,G/T and N,N,N and N,N,A/C).

In a general sense, saturation mutagenesis is comprised of mutagenizinga complete set of mutagenic cassettes (wherein each cassette ispreferably 1-500 bases in length) in defined polynucleotide sequence tobe mutagenized (wherein the sequence to be mutagenized is preferablyfrom 15 to 100,000 bases in length). Thusly, a group of mutations(ranging from 1 to 100 mutations) is introduced into each cassette to bemutagenized. A grouping of mutations to be introduced into one cassettecan be different or the same from a second grouping of mutations to beintroduced into a second cassette during the application of one round ofsaturation mutagenesis. Such groupings are exemplified by deletions,additions, groupings of particular codons, and groupings of particularnucleotide cassettes.

Defined sequences to be mutagenized (see FIG. 20) include preferably awhole gene, pathway, cDNA, an entire open reading frame (ORF), andentire promoter, enhancer, repressor/transactivator, origin ofreplication, intron, operator, or any polynucleotide functional group.Generally, a preferred “defined sequences” for this purpose may be anypolynucleotide that a 15 base-polynucleotide sequence, andpolynucleotide sequences of lengths between 15 bases and 15,000 bases(this invention specifically names every integer in between).Considerations in choosing groupings of codons include types of aminoacids encoded by a degenerate mutagenic cassette.

In a particularly preferred exemplification a grouping of mutations thatcan be introduced into a mutagenic cassette (see Tables 1-85), thisinvention specifically provides for degenerate codon substitutions(using degenerate oligos) that code for 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, and 20 amino acids at each position, anda library of polypeptides encoded thereby.

Summary of Tables 1-85

These tables show preferred, but non-limiting, examples of 3-base longmutagenic cassettes that are non-stochastic and degenerate.

TABLE# triplet sequence Site 1 Site 2 Site 3 1. N, N, G/T N N G/T 2. N,N, G/C N N G/C 3. N, N, G/A N N G/A 4. N, N, A/C N N A/C 5. N, N, A/T NN A/T 6. N, N, C/T N N C/T 7. N, N, N N N N 8. N, N, G N N G 9. N, N, AN N A 10. N, N, C N N C 11. N, N, T N N T 12. N, N, C/G/T N N C/G/T 13.N, N, A/G/T N N A/G/T 14. N, N, A/C/T N N A/C/T 15. N, N, A/C/G N NA/C/G 16. N, A, A N A A 17. N, A, C N A C 18. N, A, G N A G 19. N, A, TN A T 20. N, C, A N C A 21. N, C, C N C C 22. N, C, G N C G 23. N, C, TN C T 24. N, G, A N G A 25. N, G, C N G C 26. N, G, G N G G 27. N, G, TN G T 28. N, T, A N T A 29. N, T, C N T C 30. N, T, G N T G 31. N, T, TN T T 32. N, A/C, A N A/C A 33. N, A/G, A N A/G A 34. N, A/T, A N A/T A35. N, C/G, A N C/G A 36. N, C/T, A N C/T A 37. N, T/G, A N T/G A 38. N,C/G/T, A N C/G/T A 39. N, A/G/T, A N A/G/T A 40. N, A/C/T, A N A/C/T A41. N, A/C/G, A N A/C/G A 42. A, N, N A N N 43. C, N, N C N N 44. G, N,N G N N 45. T, N, N T N N 46. A/C, N, N A/C N N 47. A/G, N, N A/G N N48. A/T, N, N A/T N N 49. C/G, N, N C/G N N 50. C/T, N, N C/T N N 51.G/T, N, N G/T N N 52. N, A, N N A N 53. N, C, N N C N 54. N, G, N N G N55. N, T, N N T N 56. N, A/C, N N A/C N 57. N, A/G, N N A/G N 58. N,A/T, N N A/T N 59. N, C/G, N N C/G N 60. N, C/T, N N C/T N 61. N, G/T, NN G/T N 62. N, A/C/G, N N A/C/G N 63. N, A/C/T, N N A/C/T N 64. N,A/G/T, N N A/G/T N 65. N, C/G/T, N N C/G/T N 66. C, C, N C C N 67. G, G,N G G N 68. G, C, N G C N 69. G, T, N G T N 70. C, G, N C G N 71. C, T,N C T N 72. T, C, N T C N 73. A, C, N A C N 74. G, A, N G A N 75. A, T,N A T N 76. C, A, N C A N 77. T, T, N T T N 78. A, A, N A A N 79. T, A,N T A N 80. T, G, N T G N 81. A, G, N A G N 82. G/C, G, N G/C G N 83.G/C, C, N G/C C N 84. G/C, A, N G/C A N 85. G/C, T, N G/C T N

TABLE 1 Mutagenic Cassette: N, N, G/T CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 2 NONPOLAR 15 GGC NO(NPL) GGA NO GGG YES GCT YES ALANINE 2 GCC NO GCA NO GCG YES GTT YESVALINE 2 GTC NO GTA NO GTG YES TTA NO LEUCINE 3 TTG YES CTT YES CTC NOCTA NO CTG YES ATT YES ISOLEUCINE 1 ATC NO ATA NO ATG YES METHIONINE 1TTT YES PHENYLALANINE 1 TTC NO TGG YES TRYPTOPHAN 1 CCT YES PROLINE 2CCC NO CCA NO CCG YES TCT YES SERINE 3 POLAR 9 TCC NO NONIONIZABLE TCANO (POL) TCG YES AGT YES AGC NO TGT YES CYSTEINE 1 TGC NO AAT YESASPARAGINE 1 AAC NO CAA NO GLUTAMINE 1 CAG YES TAT YES TYROSINE 1 TAC NOACT YES THREONINE 2 ACC NO ACA NO ACG YES GAT YES ASPARTIC ACID 1IONIZABLE: ACIDIC 2 GAC NO NEGATIVE CHARGE GAA NO GLUTAMIC ACID 1 (NEG)GAG YES AAA NO LYSINE 1 IONIZABLE: BASIC 5 AAG YES POSITIVE CHARGE CGTYES ARGININE 3 (POS) CGC NO CGA NO CGG YES AGA NO AGG YES CAT YESHISTIDINE 1 CAC NO TAA NO STOP CODON 1 STOP SIGNAL 1 TAG YES (STP) TGANO TOTAL 32 20 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 6415: 9: 2: 5: 1

TABLE 2 Mutagenic Cassette: N, N, G/C CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT NO GLYCINE 2 NONPOLAR 15 GGC YES(NPL) GGA NO GGG YES GCT NO ALANINE 2 GCC YES GCA NO GCG YES GTT NOVALINE 2 GTC YES GTA NO GTG YES TTA NO LEUCINE 3 TTG YES CTT NO CTC YESCTA NO CTG YES ATT NO ISOLEUCINE 1 ATC YES ATA NO ATG YES METHIONINE 1TTT NO PHENYLALANINE 1 TTC YES TGG YES TRYPTOPHAN 1 CCT NO PROLINE 2 CCCYES CCA NO CCG YES TCT NO SERINE 3 POLAR 9 TCC YES NONIONIZABLE TCA NO(POL) TCG YES AGT NO AGC YES TGT NO CYSTEINE 1 TGC YES AAT NO ASPARAGINE1 AAC YES CAA NO GLUTAMINE 1 CAG YES TAT NO TYROSINE 1 TAC YES ACT NOTHREONINE 2 ACC YES ACA NO ACG YES GAT NO ASPARTIC ACID 1 IONIZABLE:ACIDIC 2 GAC YES NEGATIVE CHARGE GAA NO GLUTAMIC ACID 1 (NEG) GAG YESAAA NO LYSINE 1 IONIZABLE: BASIC 5 AAG YES POSITIVE CHARGE CGT NOARGININE 3 (POS) CGC YES CGA NO CGG YES AGA NO AGG YES CAT NO HISTIDINE1 CAC YES TAA NO STOP CODON 1 STOP SIGNAL 1 TAG YES (STP) TGA NO TOTAL32 20 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 64 15: 9: 2:5: 1

TABLE 3 Mutagenic Cassette: N, N, G/A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT NO GLYCINE 2 NONPOLAR 15 GGC NO(NPL) GGA YES GGG YES GCT NO ALANINE 2 GCC NO GCA YES GCG YES GTT NOVALINE 2 GTC NO GTA YES GTG YES TTA YES LEUCINE 4 TTG YES CTT NO CTC NOCTA YES CTG YES ATT NO ISOLEUCINE 1 ATC NO ATA YES ATG YES METHIONINE 1TTT NO PHENYLALANINE 0 TTC NO TGG YES TRYPTOPHAN 1 CCT NO PROLINE 2 CCCNO CCA YES CCG YES TCT NO SERINE 2 POLAR 6 TCC NO NONIONIZABLE TCA YES(POL) TCG YES AGT NO AGC NO TGT NO CYSTEINE 0 TGC NO AAT NO ASPARAGINE 0AAC NO CAA YES GLUTAMINE 2 CAG YES TAT NO TYROSINE 0 TAC NO ACT NOTHREONINE 2 ACC NO ACA YES ACG YES GAT NO ASPARTIC ACID 0 IONIZABLE:ACIDIC 2 GAC NO NEGATIVE CHARGE GAA YES GLUTAMIC ACID 2 (NEG) GAG YESAAA YES LYSINE 2 IONIZABLE: BASIC 6 AAG YES POSITIVE CHARGE CGT NOARGININE 4 (POS) CGC NO CGA YES CGG YES AGA YES AGG YES CAT NO HISTIDINE0 CAC NO TAA YES STOP CODON 3 STOP SIGNAL 3 TAG YES (STP) TGA YES TOTAL32 14 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 64 15: 6: 2:6: 3

TABLE 4 Mutagenic Cassette: N, N, A/C CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT NO GLYCINE 2 NONPOLAR 14 GGC YES(NPL) GGA YES GGG NO GCT NO ALANINE 2 GCC YES GCA YES GCG NO GTT NOVALINE 2 GTC YES GTA YES GTG NO TTA YES LEUCINE 3 TTG NO CTT NO CTC YESCTA YES CTG NO ATT NO ISOLEUCINE 2 ATC YES ATA YES ATG NO METHIONINE 0TTT NO PHENYLALANINE 1 TTC YES TGG NO TRYPTOPHAN 0 CCT NO PROLINE 2 CCCYES CCA YES CCG NO TCT NO SERINE 3 POLAR 9 TCC YES NONIONIZABLE TCA YES(POL) TCG NO AGT NO AGC YES TGT NO CYSTEINE 1 TGC YES AAT NO ASPARAGINE1 AAC YES CAA YES GLUTAMINE 1 CAG NO TAT NO TYROSINE 1 TAC YES ACT NOTHREONINE 2 ACC YES ACA YES ACG NO GAT NO ASPARTIC ACID 1 IONIZABLE:ACIDIC 2 GAC YES NEGATIVE CHARGE GAA YES GLUTAMIC ACID 1 (NEG) GAG NOAAA YES LYSINE 1 IONIZABLE: BASIC 5 AAG NO POSITIVE CHARGE CGT NOARGININE 3 (POS) CGC YES CGA YES CGG NO AGA YES AGG NO CAT NO HISTIDINE1 CAC YES TAA YES STOP CODON 2 STOP SIGNAL 2 TAG NO (STP) TGA YES TOTAL32 18 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 64 14: 9: 2:5: 2

TABLE 5 Mutagenic Cassette: N, N, A/T CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 2 NONPOLAR 14 GGC NO(NPL) GGA YES GGG NO GCT YES ALANINE 2 GCC NO GCA YES GCG NO GTT YESVALINE 2 GTC NO GTA YES GTG NO TTA YES LEUCINE 3 TTG NO CTT YES CTC NOCTA YES CTG NO ATT YES ISOLEUCINE 2 ATC NO ATA YES ATG NO METHIONINE 0TTT YES PHENYLALANINE 1 TTC NO TGG NO TRYPTOPHAN 0 CCT YES PROLINE 2 CCCNO CCA YES CCG NO TCT YES SERINE 3 POLAR 9 TCC NO NONIONIZABLE TCA YES(POL) TCG NO AGT YES AGC NO TGT YES CYSTEINE 1 TGC NO AAT YES ASPARAGINE1 AAC NO CAA YES GLUTAMINE 1 CAG NO TAT YES TYROSINE 1 TAC NO ACT YESTHREONINE 2 ACC NO ACA YES ACG NO GAT YES ASPARTIC ACID 1 IONIZABLE:ACIDIC 2 GAC NO NEGATIVE CHARGE GAA YES GLUTAMIC ACID 1 (NEG) GAG NO AAAYES LYSINE 1 IONIZABLE: BASIC 5 AAG NO POSITIVE CHARGE CGT YES ARGININE3 (POS) CGC NO CGA YES CGG NO AGA YES AGG NO CAT YES HISTIDINE 1 CAC NOTAA YES STOP CODON 2 STOP SIGNAL 2 TAG NO (STP) TGA YES TOTAL 32 18Amino Acids Are Represented NPL: POL: NEG: POS: STP = 64 14: 9: 2: 5: 2

TABLE 6 Mutagenic Cassette: N, N, C/T CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 2 NONPOLAR 14 GGC YES(NPL) GGA NO GGG NO GCT YES ALANINE 2 GCC YES GCA NO GCG NO GTT YESVALINE 2 GTC YES GTA NO GTG NO TTA NO LEUCINE 2 TTG NO CTT YES CTC YESCTA NO CTG NO ATT YES ISOLEUCINE 2 ATC YES ATA NO ATG NO METHIONINE 0TTT YES PHENYLALANINE 2 TTC YES TGG NO TRYPTOPHAN 0 CCT YES PROLINE 2CCC YES CCA NO CCG NO TCT YES SERINE 4 POLAR 12 TCC YES NONIONIZABLE TCANO (POL) TCG NO AGT YES AGC YES TGT YES CYSTEINE 2 TGC YES AAT YESASPARAGINE 2 AAC YES CAA NO GLUTAMINE 0 CAG NO TAT YES TYROSINE 2 TACYES ACT YES THREONINE 2 ACC YES ACA NO ACG NO GAT YES ASPARTIC ACID 2IONIZABLE: ACIDIC 2 GAC YES NEGATIVE CHARGE GAA NO GLUTAMIC ACID 0 (NEG)GAG NO AAA NO LYSINE 0 IONIZABLE: BASIC 4 AAG NO POSITIVE CHARGE CGT YESARGININE 2 (POS) CGC YES CGA NO CGG NO AGA NO AGG NO CAT YES HISTIDINE 2CAC YES TAA NO STOP CODON 0 STOP SIGNAL 0 TAG NO (STP) TGA NO TOTAL 3215 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 64 14: 12: 2:4: 0

TABLE 7 Mutagenic Cassette: N, N, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 4 NONPOLAR 29 GGC YES(NPL) GGA YES GGG YES GCT YES ALANINE 4 GCC YES GCA YES GCG YES GTT YESVALINE 4 GTC YES GTA YES GTG YES TTA YES LEUCINE 6 TTG YES CTT YES CTCYES CTA YES CTG YES ATT YES ISOLEUCINE 3 ATC YES ATA YES ATG YESMETHIONINE 1 TTT YES PHENYLALANINE 2 TTC YES TGG YES TRYPTOPHAN 1 CCTYES PROLINE 4 CCC YES CCA YES CCG YES TCT YES SERINE 6 POLAR 18 TCC YESNONIONIZABLE TCA YES (POL) TCG YES AGT YES AGC YES TGT YES CYSTEINE 2TGC YES AAT YES ASPARAGINE 2 AAC YES CAA YES GLUTAMINE 2 CAG YES TAT YESTYROSINE 2 TAC YES ACT YES THREONINE 4 ACC YES ACA YES ACG YES GAT YESASPARTIC ACID 2 IONIZABLE: ACIDIC 4 GAC YES NEGATIVE CHARGE GAA YESGLUTAMIC ACID 2 (NEG) GAG YES AAA YES LYSINE 2 IONIZABLE: BASIC 10 AAGYES POSITIVE CHARGE CGT YES ARGININE 6 (POS) CGC YES CGA YES CGG YES AGAYES AGG YES CAT YES HISTIDINE 2 CAC YES TAA YES STOP CODON 3 STOP SIGNAL3 TAG YES (STP) TGA YES TOTAL 64 20 Amino Acids Are Represented NPL:POL: NEG: POS: STP = 64 29: 18: 4: 10: 3

TABLE 8 Mutagenic Cassette: N, N, G CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT NO GLYCINE 1 NONPOLAR 8 GGC NO(NPL) GGA NO GGG YES GCT NO ALANINE 1 GCC NO GCA NO GCG YES GTT NOVALINE 1 GTC NO GTA NO GTG YES TTA NO LEUCINE 2 TTG YES CTT NO CTC NOCTA NO CTG YES ATT NO ISOLEUCINE 0 ATC NO ATA NO ATG YES METHIONINE 1TTT NO PHENYLALANINE 0 TTC NO TGG YES TRYPTOPHAN 1 CCT NO PROLINE 1 CCCNO CCA NO CCG YES TCT NO SERINE 1 POLAR 3 TCC NO NONIONIZABLE TCA NO(POL) TCG YES AGT NO AGC NO TGT NO CYSTEINE 0 TGC NO AAT NO ASPARAGINE 0AAC NO CAA NO GLUTAMINE 1 CAG YES TAT NO TYROSINE 0 TAC NO ACT NOTHREONINE 1 ACC NO ACA NO ACG YES GAT NO ASPARTIC ACID 0 IONIZABLE:ACIDIC 1 GAC NO NEGATIVE CHARGE GAA NO GLUTAMIC ACID 1 (NEG) GAG YES AAANO LYSINE 1 IONIZABLE: BASIC 3 AAG YES POSITIVE CHARGE CGT NO ARGININE 2(POS) CGC NO CGA NO CGG YES AGA NO AGG YES CAT NO HISTIDINE 0 CAC NO TAANO STOP CODON 1 STOP SIGNAL 1 TAG YES (STP) TGA NO TOTAL 16 13 AminoAcids Are Represented NPL: POL: NEG: POS: STP = 64 8: 3: 1: 3: 1

TABLE 9 Mutagenic Cassette: N, N, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT NO GLYCINE 1 NONPOLAR 7 GGC NO(NPL) GGA YES GGG NO GCT NO ALANINE 1 GCC NO GCA YES GCG NO GTT NOVALINE 1 GTC NO GTA YES GTG NO TTA YES LEUCINE 2 TTG NO CTT NO CTC NOCTA YES CTG NO ATT NO ISOLEUCINE 1 ATC NO ATA YES ATG NO METHIONINE 0TTT NO PHENYLALANINE 0 TTC NO TGG NO TRYPTOPHAN 0 CCT NO PROLINE 1 CCCNO CCA YES CCG NO TCT NO SERINE 1 POLAR 3 TCC NO NONIONIZABLE TCA YES(POL) TCG NO AGT NO AGC NO TGT NO CYSTEINE 0 TGC NO AAT NO ASPARAGINE 0AAC NO CAA YES GLUTAMINE 1 CAG NO TAT NO TYROSINE 0 TAC NO ACT NOTHREONINE 1 ACC NO ACA YES ACG NO GAT NO ASPARTIC ACID 0 IONIZABLE:ACIDIC 1 GAC NO NEGATIVE CHARGE GAA YES GLUTAMIC ACID 1 (NEG) GAG NO AAAYES LYSINE 1 IONIZABLE: BASIC 3 AAG NO POSITIVE CHARGE CGT NO ARGININE 2(POS) CGC NO CGA YES CGG NO AGA YES AGG NO CAT NO HISTIDINE 0 CAC NO TAAYES STOP CODON 2 STOP SIGNAL 2 TAG NO (STP) TGA YES TOTAL 16 12 AminoAcids Are Represented NPL: POL: NEG: POS: STP = 64 7: 3: 1: 3: 2

TABLE 10 Mutagenic Cassette: N, N, C CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT NO GLYCINE 1 NONPOLAR 7 GGC YES(NPL) GGA NO GGG NO GCT NO ALANINE 1 GCC YES GCA NO GCG NO GTT NO VALINE1 GTC YES GTA NO GTG NO TTA NO LEUCINE 1 TTG NO CTT NO CTC YES CTA NOCTG NO ATT NO ISOLEUCINE 1 ATC YES ATA NO ATG NO METHIONINE 0 TTT NOPHENYLALANINE 1 TTC YES TGG NO TRYPTOPHAN 0 CCT NO PROLINE 1 CCC YES CCANO CCG NO TCT NO SERINE 2 POLAR 6 TCC YES NONIONIZABLE TCA NO (POL) TCGNO AGT NO AGC YES TGT NO CYSTEINE 1 TGC YES AAT NO ASPARAGINE 1 AAC YESCAA NO GLUTAMINE 0 CAG NO TAT NO TYROSINE 1 TAC YES ACT NO THREONINE 1ACC YES ACA NO ACG NO GAT NO ASPARTIC ACID 1 IONIZABLE: ACIDIC 1 GAC YESNEGATIVE CHARGE GAA NO GLUTAMIC ACID 0 (NEG) GAG NO AAA NO LYSINE 0IONIZABLE: BASIC 2 AAG NO POSITIVE CHARGE CGT NO ARGININE 1 (POS) CGCYES CGA NO CGG NO AGA NO AGG NO CAT NO HISTIDINE 1 CAC YES TAA NO STOPCODON 0 STOP SIGNAL 0 TAG NO (STP) TGA NO TOTAL 16 15 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 64 7: 6: 1: 2: 0

TABLE 11 Mutagenic Cassette: N, N, T CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 1 NONPOLAR 7 GGC NO(NPL) GGA NO GGG NO GCT YES ALANINE 1 GGC NO GCA NO GCG NO GTT YESVALINE 1 GTC NO GTA NO GTG NO TTA NO LEUCINE 1 TTG NO CTT YES CTC NO CTANO CTG NO ATT YES ISOLEUCINE 1 ATC NO ATA NO ATG NO METHIONINE 0 TTT YESPHENYLALANINE 1 TTC NO TGG NO TRYPTOPHAN 0 CCT YES PROLINE 1 CCC NO CCANO CCG NO TCT YES SERINE 2 POLAR 6 TCC NO NONIONIZABLE TCA NO (POL) TCGNO AGT YES AGC NO TGT YES CYSTEINE 1 TGC NO AAT YES ASPARAGINE 1 AAC NOCAA NO GLUTAMINE 0 CAG NO TAT YES TYROSINE 1 TAC NO ACT YES THREONINE 1ACC NO ACA NO ACG NO GAT YES ASPARTIC ACID 1 IONIZABLE: ACIDIC 1 GAC NONEGATIVE CHARGE GAA NO GLUTAMIC ACID 0 (NEG) GAG NO AAA NO LYSINE 0IONIZABLE: BASIC 2 AAG NO POSITIVE CHARGE CGT YES ARGININE 1 (POS) CGCNO CGA NO CGG NO AGA NO AGG NO CAT YES HISTIDINE 1 CAC NO TAA NO STOPCODON 0 STOP SIGNAL 0 TAG NO (STP) TGA NO TOTAL 16 15 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 64 7: 6: 1: 2: 0

TABLE 12 Mutagenic Cassette: N, N, C/G/T CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 3 NONPOLAR 22 GGC YES(NPL) GGA NO GGG YES GCT YES ALANINE 3 GCC YES GCA NO GCG YES GTT YESVALINE 3 GTC YES GTA NO GTG YES TTA NO LEUCINE 4 TTG YES CTT YES CTC YESCTA NO CTG YES ATT YES ISOLEUCINE 2 ATC YES ATA NO ATG YES METHIONINE 1TTT YES PHENYLALANINE 2 TTC YES TGG YES TRYPTOPHAN 1 CCT YES PROLINE 3CCC YES CCA NO CCG YES TCT YES SERINE 5 POLAR 15 TCC YES NONIONIZABLETCA NO (POL) TCG YES AGT YES AGC YES TGT YES CYSTEINE 2 TGC YES AAT YESASPARAGINE 2 AAC YES CAA NO GLUTAMINE 1 CAG YES TAT YES TYROSINE 2 TACYES ACT YES THREONINE 3 ACC YES ACA NO ACG YES GAT YES ASPARTIC ACID 2IONIZABLE: ACIDIC 3 GAC YES NEGATIVE CHARGE GAA NO GLUTAMIC ACID 1 (NEG)GAG YES AAA NO LYSINE 1 IONIZABLE: BASIC 7 AAG YES POSITIVE CHARGE CGTYES ARGININE 4 (POS) CGC YES CGA NO CGG YES AGA NO AGG YES CAT YESHISTIDINE 2 CAC YES TAA NO STOP CODON 1 STOP SIGNAL 1 TAG YES (STP) TGANO TOTAL 48 20 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 6422: 15: 3: 7: 1

TABLE 13 Mutagenic Cassette: N, N, A/G/T CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 3 NONPOLAR 22 GGC NO(NPL) GGA YES GGG YES GCT YES ALANINE 3 GCC NO GCA YES GCG YES GTT YESVALINE 3 GTC NO GTA YES GTG YES TTA YES LEUCINE 5 TTG YES CTT YES CTC NOCTA YES CTG YES ATT YES ISOLEUCINE 2 ATC NO ATA YES ATG YES METHIONINE 1TTT YES PHENYLALANINE 1 TTC NO TGG YES TRYPTOPHAN 1 CCT YES PROLINE 3CCC NO CCA YES CCG YES TCT YES SERINE 4 POLAR 12 TCC NO NONIONIZABLE TCAYES (POL) TCG YES AGT YES AGC NO TGT YES CYSTEINE 1 TGC NO AAT YESASPARAGINE 1 AAC NO CAA YES GLUTAMINE 2 CAG YES TAT YES TYROSINE 1 TACNO ACT YES THREONINE 3 ACC NO ACA YES ACG YES GAT YES ASPARTIC ACID 1IONIZABLE: ACIDIC 3 GAC NO NEGATIVE CHARGE GAA YES GLUTAMIC ACID 2 (NEG)GAG YES AAA YES LYSINE 2 IONIZABLE: BASIC 8 AAG YES POSITIVE CHARGE CGTYES ARGININE 5 (POS) CGC NO CGA YES CGG YES AGA YES AGG YES CAT YESHISTIDINE 1 CAC NO TAA YES STOP CODON 3 STOP SIGNAL 3 TAG YES (STP) TGAYES TOTAL 48 20 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 6422: 12: 3: 8: 3

TABLE 14 Mutagenic Cassette: N, N, A/C/T CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 3 NONPOLAR 21 GGC YES(NPL) GGA YES GGG NO GCT YES ALANINE 3 GCC YES GCA YES GCG NO GTT YESVALINE 3 GTC YES GTA YES GTG NO TTA YES LEUCINE 4 TTG NO CTT YES CTC YESCTA YES CTG NO ATT YES ISOLEUCINE 3 ATC YES ATA YES ATG NO METHIONINE 0TTT YES PHENYLALANINE 2 TTC YES TGG NO TRYPTOPHAN 0 CCT YES PROLINE 3CCC YES CCA YES CCG NO TCT YES SERINE 5 POLAR 15 TCC YES NONIONIZABLETCA YES (POL) TCG NO AGT YES AGC YES TGT YES CYSTEINE 2 TGC YES AAT YESASPARAGINE 2 AAC YES CAA YES GLUTAMINE 1 CAG NO TAT YES TYROSINE 2 TACYES ACT YES THREONINE 3 ACC YES ACA YES ACG NO GAT YES ASPARTIC ACID 2IONIZABLE: ACIDIC 3 GAC YES NEGATIVE CHARGE GAA YES GLUTAMIC ACID 1(NEG) GAG NO AAA YES LYSINE 1 IONIZABLE: BASIC 7 AAG NO POSITIVE CHARGECGT YES ARGININE 4 (POS) CGC YES CGA YES CGG NO AGA YES AGG NO CAT YESHISTIDINE 2 CAC YES TAA YES STOP CODON 2 STOP SIGNAL 2 TAG NO (STP) TGAYES TOTAL 48 18 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 6421: 15: 3: 7: 2

TABLE 15 Mutagenic Cassette: N, N, A/C/G CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT NO GLYCINE 3 NONPOLAR 22 GGC YES(NPL) GGA YES GGG YES GCT NO ALANINE 3 GCC YES GCA YES GCG YES GTT NOVALINE 3 GTC YES GTA YES GTG YES TTA YES LEUCINE 5 TTG YES CTT NO CTCYES CTA YES CTG YES ATT NO ISOLEUCINE 2 ATC YES ATA YES ATG YESMETHIONINE 1 TTT NO PHENYLALANINE 1 TTC YES TGG YES TRYPTOPHAN 1 CCT NOPROLINE 3 CCC YES CCA YES CCG YES TCT NO SERINE 4 POLAR 12 TCC YESNONIONIZABLE TCA YES (POL) TCG YES AGT NO AGC YES TGT NO CYSTEINE 1 TGCYES AAT NO ASPARAGINE 1 AAC YES CAA YES GLUTAMINE 2 CAG YES TAT NOTYROSINE 1 TAC YES ACT NO THREONINE 3 ACC YES ACA YES ACG YES GAT NOASPARTIC ACID 1 IONIZABLE: ACIDIC 3 GAC YES NEGATIVE CHARGE GAA YESGLUTAMIC ACID 2 (NEG) GAG YES AAA YES LYSINE 2 IONIZABLE: BASIC 8 AAGYES POSITIVE CHARGE CGT NO ARGININE 5 (POS) CGC YES CGA YES CGG YES AGAYES AGG YES CAT NO HISTIDINE 1 CAC YES TAA YES STOP CODON 3 STOP SIGNAL3 TAG YES (STP) TGA YES TOTAL 48 20 Amino Acids Are Represented NPL:POL: NEG: POS: STP = 64 22: 12: 3: 8: 3

TABLE 16 Mutagenic Cassette: N, A, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 0 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 PROLINE 0 SERINE 0 POLAR 1 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL)CAA YES GLUTAMINE 1 TYROSINE 0 THREONINE 0 ASPARTIC ACID 0 IONIZABLE:ACIDIC 1 GAA YES GLUTAMIC ACID 1 NEGATIVE CHARGE (NEG) AAA YES LYSINE 1IONIZABLE: BASIC 1 ARGININE 0 POSITIVE CHARGE HISTIDINE 0 (POS) TAA YESSTOP CODON 1 STOP SIGNAL 1 (STP) TOTAL 4 3 Amino Acids Are RepresentedNPL: POL: NEG: POS: STP = 0: 1: 1: 1: 1

TABLE 17 Mutagenic Cassette: N, A, C CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 0 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 PROLINE 0 SERINE 0 POLAR 2 CYSTEINE 0 NONIONIZABLE AAC YES ASPARAGINE1 (POL) GLUTAMINE 0 TAC YES TYROSINE 1 THREONINE 0 GAC YES ASPARTIC ACID1 IONIZABLE: ACIDIC 1 GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE 0IONIZABLE: BASIC 1 ARGININE 0 POSITIVE CHARGE CAC YES HISTIDINE 1 (POS)STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 4 Amino Acids Are RepresentedNPL: POL: NEG: POS: STP = 0: 2: 1: 1: 0

TABLE 18 Mutagenic Cassette: N, A, G CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 0 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 PROLINE 0 SERINE 0 POLAR 1 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL)CAG YES GLUTAMINE 1 TYROSINE 0 THREONINE 0 ASPARTIC ACID 0 IONIZABLE:ACIDIC 1 GAG YES GLUTAMIC ACID 1 NEGATIVE CHARGE (NEG) AAG YES LYSINE 1IONIZABLE: BASIC 1 ARGININE 0 POSITIVE CHARGE HISTIDINE 0 (POS) TAG YESSTOP CODON 1 STOP SIGNAL 1 (STP) TOTAL 4 3 Amino Acids Are RepresentedNPL: POL: NEG: POS: STP = 0: 1: 1: 1: 1

TABLE 19 Mutagenic Cassette: N, A, T CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 0 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 PROLINE 0 SERINE 0 POLAR 2 CYSTEINE 0 NONIONIZABLE AAT YES ASPARAGINE1 (POL) GLUTAMINE 0 TAT YES TYROSINE 1 THREONINE 0 GAT YES ASPARTIC ACID1 IONIZABLE: ACIDIC 1 GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE 0IONIZABLE: BASIC 1 ARGININE 0 POSITIVE CHARGE CAT YES HISTIDINE 1 (POS)STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 4 Amino Acids Are RepresentedNPL: POL: NEG: POS: STP = 0: 2: 1: 1: 0

TABLE 20 Mutagenic Cassette: N, C, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 2 GCA YES ALANINE 1(NPL) VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0TRYPTOPHAN 0 CCA YES PROLINE 1 TCA YES SERINE 1 POLAR 2 CYSTEINE 0NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0 ACA YES THREONINE1 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0(POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 4 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 2: 2: 0: 0: 0

TABLE 21 Mutagenic Cassette: N, C, C CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 2 GCC YES ALANINE 1(NPL) VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0TRYPTOPHAN 0 CCC YES PROLINE 1 TCC YES SERINE 1 POLAR 2 CYSTEINE 0NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0 ACC YES THREONINE1 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0(POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 4 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 2: 2: 0: 0: 0

TABLE 22 Mutagenic Cassette: N, C, G CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 2 GCG YES ALANINE 1(NPL) VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0TRYPTOPHAN 0 CCG YES PROLINE 1 TCG YES SERINE 1 POLAR 2 CYSTEINE 0NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0 ACG YES THREONINE1 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0(POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 4 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 2: 2: 0: 0: 0

TABLE 23 Mutagenic Cassette: N, C, T CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 2 GCT YES ALANINE 1(NPL) VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0TRYPTOPHAN 0 CCT YES PROLINE 1 TCT YES SERINE 1 POLAR 2 CYSTEINE 0NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0 ACT YES THREONINE1 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0(POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 4 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 2: 2: 0: 0: 0

TABLE 24 Mutagenic Cassette: N, G, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGA YES GLYCINE 1 NONPOLAR 1 ALANINE 0(NPL) VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 0 CYSTEINE 0 NONIONIZABLEASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0 THREONINE 0 ASPARTIC ACID 0IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE 0IONIZABLE: BASIC 2 CGA YES ARGININE 2 POSITIVE CHARGE AGA YES (POS)HISTIDINE 0 TGA YES STOP CODON 1 STOP SIGNAL 1 (STP) TOTAL 4 2 AminoAcids Are Represented NPL: POL: NEG: POS: STP = 1: 0: 0: 2: 1

TABLE 25 Mutagenic Cassette: N, G, C CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGC YES GLYCINE 1 NONPOLAR 1 ALANINE 0(NPL) VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0TRYPTOPHAN 0 PROLINE 0 AGC YES SERINE 1 POLAR 2 TGC YES CYSTEINE 1NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0 THREONINE 0ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) LYSINE 0 IONIZABLE: BASIC 1 CGC YES ARGININE 1 POSITIVE CHARGEHISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 4 Amino AcidsAre Represented NPL: POL: NEG: POS: STP = 1: 2: 0: 1: 0

TABLE 26 Mutagenic Cassette: N, G, G CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGG YES GLYCINE 1 NONPOLAR 2 ALANINE 0(NPL) VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TGGYES TRYPTOPHAN 1 PROLINE 0 SERINE 0 POLAR 0 CYSTEINE 0 NONIONIZABLEASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0 THREONINE 0 ASPARTIC ACID 0IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE 0IONIZABLE: BASIC 2 CGG YES ARGININE 2 POSITIVE CHARGE AGG YES (POS)HISTIDINE 0 STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 3 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 2: 0: 0: 2: 0

TABLE 27 Mutagenic Cassette: N, G, T CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 1 NONPOLAR 1 ALANINE 0(NPL) VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0TRYPTOPHAN 0 PROLINE 0 AGT YES SERINE 1 POLAR 2 TGT YES CYSTEINE 1NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0 THREONINE 0ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) LYSINE 0 IONIZABLE: BASIC 1 CGT YES ARGININE 1 POSITIVE CHARGEHISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 4 Amino AcidsAre Represented NPL: POL: NEG: POS: STP = 1: 2: 0: 1: 0

TABLE 28 Mutagenic Cassette: N, T, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 4 ALANINE 0 (NPL)GTA YES VALINE 1 TTA YES LEUCINE 2 CTA YES ATA YES ISOLEUCINE 1METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 0CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVECHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGEHISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 3 Amino AcidsAre Represented NPL: POL: NEG: POS: STP = 4: 0: 0: 0: 0

TABLE 29 Mutagenic Cassette: N, T, C CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 4 ALANINE 0 (NPL)GTC YES VALINE 1 CTC YES LEUCINE 1 ATC YES ISOLEUCINE 1 METHIONINE 0 TTCYES PHENYLALANINE 1 TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 0 CYSTEINE 0NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0 THREONINE 0ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0(POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 4 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 4: 0: 0: 0: 0

TABLE 30 Mutagenic Cassette: N, T, G CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 4 ALANINE 0 (NPL)GTG YES VALINE 1 TTG YES LEUCINE 2 CTG YES ISOLEUCINE 0 ATG YESMETHIONINE 1 PHENYLALANINE 0 TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 0CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVECHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGEHISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 3 Amino AcidsAre Represented NPL POL NEG POS: STP = 4: 0: 0: 0: 0

TABLE 31 Mutagenic Cassette: N, T, T CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 4 ALANINE 0 (NPL)GTT YES VALINE 1 CTT YES LEUCINE 1 ATT YES ISOLEUCINE 1 METHIONINE 0 TTTYES PHENYLALANINE 1 TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 0 CYSTEINE 0NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0 THREONINE 0ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0(POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 4 Amino Acids AreRepresented NPL POL NEG POS: STP = 4: 0: 0: 0: 0

TABLE 32 Mutagenic Cassette: N, A/C, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 2 GCA YES ALANINE 1(NPL) VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0TRYPTOPHAN 0 CCA YES PROLINE 1 TCA YES SERINE 1 POLAR 3 CYSTEINE 0NONIONIZABLE ASPARAGINE 0 (POL) CAA YES GLUTAMINE 1 TYROSINE 0 ACA YESTHREONINE 1 ASPARTIC ACID 0 IONIZABLE: ACIDIC 1 GAA YES GLUTAMIC ACID 1NEGATIVE CHARGE (NEG) AAA YES LYSINE 1 IONIZABLE: BASIC 1 ARGININE 0POSITIVE CHARGE HISTIDINE 0 (POS) TAA YES STOP CODON 1 STOP SIGNAL 1(STP) TOTAL 8 7 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 2:3: 1: 1: 1

TABLE 33 Mutagenic Cassette: N, A/G, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGA YES GLYCINE 1 NONPOLAR 1 ALANINE 0(NPL) VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 1 CYSTEINE 0 NONIONIZABLEASPARAGINE 0 (POL) CAA YES GLUTAMINE 1 TYROSINE 0 THREONINE 0 ASPARTICACID 0 IONIZABLE: ACIDIC 1 GAA YES GLUTAMIC ACID 1 NEGATIVE CHARGE (NEG)AAA YES LYSINE 1 IONIZABLE: BASIC 3 CGA YES ARGININE 2 POSITIVE CHARGEAGA YES (POS) HISTIDINE 0 TAA YES STOP CODON 2 STOP SIGNAL 2 TGA YES(STP) TOTAL 8 5 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 1:1: 1: 3: 2

TABLE 34 Mutagenic Cassette: N, A/T, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 4 ALANINE 0 (NPL)GTA YES VALINE 1 TTA YES LEUCINE 2 CTA YES ATA YES ISOLEUCINE 1METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 1CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) CAA YES GLUTAMINE 1 TYROSINE0 THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 1 GAA YES GLUTAMIC ACID1 NEGATIVE CHARGE (NEG) AAA YES LYSINE 1 IONIZABLE: BASIC 1 ARGININE 0POSITIVE CHARGE HISTIDINE 0 (POS) TAA YES STOP CODON 1 STOP SIGNAL 1(STP) TOTAL 8 6 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 4:1: 1: 1: 1

TABLE 35 Mutagenic Cassette: N, C/G, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGA YES GLYCINE 1 NONPOLAR 3 GCA YESALANINE 1 (NPL) VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0PHENYLALANINE 0 TRYPTOPHAN 0 CCA YES PROLINE 1 TCA YES SERINE 1 POLAR 2CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0 ACAYES THREONINE 1 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0NEGATIVE CHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 2 CGA YES ARGININE 2POSITIVE CHARGE AGA YES (POS) HISTIDINE 0 TGA YES STOP CODON 1 STOPSIGNAL 1 (STP) TOTAL 8 6 Amino Acids Are Represented NPL: POL: NEG: POS:STP = 3: 2: 0: 2: 1

TABLE 36 Mutagenic Cassette: N, C/T, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 6 GCA YES ALANINE 1(NPL) GTA YES VALINE 1 TTA YES LEUCINE 2 CTA YES ATA YES ISOLEUCINE 1METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN 0 CCA YES PROLINE 1 TCA YESSERINE 1 POLAR 2 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0TYROSINE 0 ACA YES THREONINE 1 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 0ARGININE 0 POSITIVE CHARGE HISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0(STP) TOTAL 8 7 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 6:2: 0: 0: 0

TABLE 37 Mutagenic Cassette: N, T/G, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGA YES GLYCINE 1 NONPOLAR 5 ALANINE 0(NPL) GTA YES VALINE 1 TTA YES LEUCINE 2 CTA YES ATA YES ISOLEUCINE 1METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 0CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVECHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 2 CGA YES ARGININE 2 POSITIVECHARGE AGA YES (POS) HISTIDINE 0 TGA YES STOP CODON 1 STOP SIGNAL 1(STP) TOTAL 8 5 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 5:0: 0: 2: 1

TABLE 38 Mutagenic Cassette: N, C/G/T, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGA YES GLYCINE 1 NONPOLAR 7 GCA YESALANINE 1 (NPL) GTA YES VALINE 1 TTA YES LEUCINE 2 CTA YES ATA YESISOLEUCINE 1 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN 0 CCA YES PROLINE 1TCA YES SERINE 1 POLAR 2 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL)GLUTAMINE 0 TYROSINE 0 ACA YES THREONINE 1 ASPARTIC ACID 0 IONIZABLE:ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE 0 IONIZABLE: BASIC2 CGA YES ARGININE 2 POSITIVE CHARGE AGA YES (POS) HISTIDINE 0 TGA YESSTOP CODON 1 STOP SIGNAL 1 (STP) TOTAL 12 9 Amino Acids Are RepresentedNPL: POL: NEG: POS: STP = 7: 2: 0: 2: 1

TABLE 39 Mutagenic Cassette: N, A/G/T, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGA YES GLYCINE 1 NONPOLAR 5 ALANINE 0(NPL) GTA YES VALINE 1 TTA YES LEUCINE 2 CTA YES ATA YES ISOLEUCINE 1METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 1CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) CAA YES GLUTAMINE 1 TYROSINE0 THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 1 GAA YES GLUTAMIC ACID1 NEGATIVE CHARGE (NEG) AAA YES LYSINE 1 IONIZABLE: BASIC 3 CGA YESARGININE 2 POSITIVE CHARGE AGA YES (POS) HISTIDINE 0 TAA YES STOP CODON2 STOP SIGNAL 2 TGA YES (STP) TOTAL 12 8 Amino Acids Are RepresentedNPL: POL: NEG: POS: STP = 5: 1: 1: 3: 2

TABLE 40 Mutagenic Cassette: N, A/C/T, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 6 GCA YES ALANINE 1(NPL) GTA YES VALINE 1 TTA YES LEUCINE 2 CTA YES ATA YES ISOLEUCINE 1METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN 0 CCA YES PROLINE 1 TCA YESSERINE 1 POLAR 3 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) CAA YESGLUTAMINE 1 TYROSINE 0 ACA YES THREONINE 1 ASPARTIC ACID 0 IONIZABLE:ACIDIC 1 GAA YES GLUTAMIC ACID 1 NEGATIVE CHARGE (NEG) AAA YES LYSINE 1IONIZABLE: BASIC 1 ARGININE 0 POSITIVE CHARGE HISTIDINE 0 (POS) TAA YESSTOP CODON 1 STOP SIGNAL 1 (STP) TOTAL 12 10 Amino Acids Are RepresentedNPL: POL: NEG: POS: STP = 6: 3: 1: 1: 1

TABLE 41 Mutagenic Cassette: N, A/C/G, A CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGA YES GLYCINE 1 NONPOLAR 3 GCA YESALANINE 1 (NPL) VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0PHENYLALANINE 0 TRYPTOPHAN 0 CCA YES PROLINE 1 TCA YES SERINE 1 POLAR 3CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) CAA YES GLUTAMINE 1 TYROSINE0 ACA YES THREONINE 1 ASPARTIC ACID 0 IONIZABLE: ACIDIC 1 GAA YESGLUTAMIC ACID 1 NEGATIVE CHARGE (NEG) AAA YES LYSINE 1 IONIZABLE: BASIC3 CGA YES ARGININE 2 POSITIVE CHARGE AGA YES (POS) HISTIDINE 0 TAA YESSTOP CODON 2 STOP SIGNAL 2 TGA YES (STP) TOTAL 12 9 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 3: 3: 1: 3: 2

TABLE 42 Mutagenic Cassette: A, N, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 4 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ATT YES ISOLEUCINE 3 ATC YES ATA YES ATG YESMETHIONINE 1 PHENYLALANINE 0 TRYPTOPHAN 0 PROLINE 0 AGT YES SERINE 2POLAR 8 AGC YES NONIONIZABLE CYSTEINE 0 (POL) AAT YES ASPARAGINE 2 AACYES GLUTAMINE 0 TYROSINE 0 ACT YES THREONINE 4 ACC YES ACA YES ACG YESASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) AAA YES LYSINE 2 IONIZABLE: BASIC 4 AAG YES POSITIVE CHARGE AGAYES ARGININE 2 (POS) AGG YES HISTIDINE 0 STOP CODON 0 STOP SIGNAL 0(STP) TOTAL 16 7 Amino Acids Are Represented NPL: POL: NEG: POS: STP =4: 8: 0: 4: 0

TABLE 43 Mutagenic Cassette: C, N, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 8 ALANINE 0 (NPL)VALINE 0 CTT YES LEUCINE 4 CTC YES CTA YES CTG YES ISOLEUCINE 0METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN 0 CCT YES PROLINE 4 CCC YES CCAYES CCG YES SERINE 0 POLAR 2 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL)CAA YES GLUTAMINE 2 CAG YES TYROSINE 0 THREONINE 0 ASPARTIC ACID 0IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE 0IONIZABLE: BASIC 6 CGT YES ARGININE 4 POSITIVE CHARGE CGC YES (POS) CGAYES CGG YES CAT YES HISTIDINE 2 CAC YES STOP CODON 0 STOP SIGNAL 0 (STP)TOTAL 16 5 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 8: 2:0: 6: 0

TABLE 44 Mutagenic Cassette: G, N, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 4 NONPOLAR 12 GGC YES(NPL) GGA YES GGG YES GCT YES ALANINE 4 GCC YES GCA YES GCG YES GTT YESVALINE 4 GTC YES GTA YES GTG YES LEUCINE 0 ISOLEUCINE 0 METHIONINE 0PHENYLALANINE 0 TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 0 CYSTEINE 0NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0 THREONINE 0 GATYES ASPARTIC ACID 2 IONIZABLE: ACIDIC 4 GAC YES NEGATIVE CHARGE GAA YESGLUTAMIC ACID 2 (NEG) GAG YES LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0POSITIVE CHARGE HISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL16 5 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 12: 0: 4: 0:0

TABLE 45 Mutagenic Cassette: T, N, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 5 ALANINE 0 (NPL)VALINE 0 TTA YES LEUCINE 2 TTG YES ISOLEUCINE 0 METHIONINE 0 TTT YESPHENYLALANINE 2 TTC YES TGG YES TRYPTOPHAN 1 PROLINE 0 TCT YES SERINE 4POLAR 8 TCC YES NONIONIZABLE TCA YES (POL) TCG YES TGT YES CYSTEINE 2TGC YES ASPARAGINE 0 GLUTAMINE 0 TAT YES TYROSINE 2 TAC YES THREONINE 0ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0(POS) TAA YES STOP CODON 3 STOP SIGNAL 3 TAG YES (STP) TGA YES TOTAL 166 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 5: 8: 0: 0: 3

TABLE 46 Mutagenic Cassette: A/C, N, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 12 ALANINE 0 (NPL)VALINE 0 CTT YES LEUCINE 4 CTC YES CTA YES CTG YES ATT YES ISOLEUCINE 3ATC YES ATA YES ATG YES METHIONINE 1 PHENYLALANINE 0 TRYPTOPHAN 0 CCTYES PROLINE 4 CCC YES CCA YES CCG YES AGT YES SERINE 2 POLAR 10 AGC YESNONIONIZABLE CYSTEINE 0 (POL) AAT YES ASPARAGINE 2 AAC YES CAA YESGLUTAMINE 2 CAG YES TYROSINE 0 ACT YES THREONINE 4 ACC YES ACA YES ACGYES ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) AAA YES LYSINE 2 IONIZABLE: BASIC 10 AAG YES POSITIVE CHARGE CGTYES ARGININE 6 (POS) CGC YES CGA YES CGG YES AGA YES AGG YES CAT YESHISTIDINE 2 CAC YES STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 32 11 AminoAcids Are Represented NPL: POL: NEG: POS: STP = 12: 10: 0: 10: 0

TABLE 47 Mutagenic Cassette: A/G, N, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 4 NONPOLAR 16 GGC YES(NPL) GGA YES GGG YES GCT YES ALANINE 4 GCC YES GCA YES GCG YES GTT YESVALINE 4 GTC YES GTA YES GTG YES LEUCINE 0 ATT YES ISOLEUCINE 3 ATC YESATA YES ATG YES METHIONINE 1 PHENYLALANINE 0 TRYPTOPHAN 0 PROLINE 0 AGTYES SERINE 2 POLAR 8 AGC YES NONIONIZABLE CYSTEINE 0 (POL) AAT YESASPARAGINE 2 AAC YES GLUTAMINE 0 TYROSINE 0 ACT YES THREONINE 4 ACC YESACA YES ACG YES GAT YES ASPARTIC ACID 2 IONIZABLE: ACIDIC 4 GAC YESNEGATIVE CHARGE GAA YES GLUTAMIC ACID 2 (NEG) GAG YES AAA YES LYSINE 2IONIZABLE: BASIC 4 AAG YES POSITIVE CHARGE AGA YES ARGININE 2 (POS) AGGYES HISTIDINE 0 STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 32 12 Amino AcidsAre Represented NPL: POL: NEG: POS: STP = 16: 8: 4: 4: 0

TABLE 48 Mutagenic Cassette: A/T, N, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 9 ALANINE 0 (NPL)VALINE 0 TTA YES LEUCINE 2 TTG YES ATT YES ISOLEUCINE 3 ATC YES ATA YESATG YES METHIONINE 1 TTT YES PHENYLALANINE 2 TTC YES TGG YES TRYPTOPHAN1 PROLINE 0 TCT YES SERINE 6 POLAR 16 TCC YES NONIONIZABLE TCA YES (POL)TCG YES AGT YES AGC YES TGT YES CYSTEINE 2 TGC YES AAT YES ASPARAGINE 2AAC YES GLUTAMINE 0 TAT YES TYROSINE 2 TAC YES ACT YES THREONINE 4 ACCYES ACA YES ACG YES ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0NEGATIVE CHARGE (NEG) AAA YES LYSINE 2 IONIZABLE: BASIC 4 AAG YESPOSITIVE CHARGE AGA YES ARGININE 2 (POS) AGG YES HISTIDINE 0 TAA YESSTOP CODON 3 STOP SIGNAL 3 (STP) TAG YES TGA YES TOTAL 32 12 Amino AcidsAre Represented NPL: POL: NEG: POS: STP = 9: 16: 0: 4: 3

TABLE 49 Mutagenic Cassette: C/G, N, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 4 NONPOLAR 20 GGC YES(NPL) GGA YES GGG YES GCT YES ALANINE 4 GCC YES GCA YES GCG YES GTT YESVALINE 4 GTC YES GTA YES GTG YES CTT YES LEUCINE 4 CTC YES CTA YES CTGYES ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN 0 CCT YESPROLINE 4 CCC YES CCA YES CCG YES SERINE 0 POLAR 2 CYSTEINE 0NONIONIZABLE ASPARAGINE 0 (POL) CAA YES GLUTAMINE 2 CAG YES TYROSINE 0THREONINE 0 GAT YES ASPARTIC ACID 2 IONIZABLE: ACIDIC 4 GAC YES NEGATIVECHARGE GAA YES GLUTAMIC ACID 2 (NEG) GAG YES LYSINE 0 IONIZABLE: BASIC 6CGT YES ARGININE 4 POSITIVE CHARGE CGC YES (POS) CGA YES CGG YES CAT YESHISTIDINE 2 CAC YES STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 32 10 AminoAcids Are Represented NPL: POL: NEG: POS: STP = 20: 2: 4: 6: 0

TABLE 50 Mutagenic Cassette: C/T, N, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 13 ALANINE 0 (NPL)VALINE 0 TTA YES LEUCINE 6 TTG YES CTT YES CTC YES CTA YES CTG YESISOLEUCINE 0 METHIONINE 0 TTT YES PHENYLALANINE 2 TTC YES TGG YESTRYPTOPHAN 1 CCT YES PROLINE 4 CCC YES CCA YES CCG YES TCT YES SERINE 4POLAR 10 TCC YES NONIONIZABLE TCA YES (POL) TCG YES TGT YES CYSTEINE 2TGC YES ASPARAGINE 0 CAA YES GLUTAMINE 2 CAG YES TAT YES TYROSINE 2 TACYES THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0NEGATIVE CHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 6 CGT YES ARGININE 4POSITIVE CHARGE CGC YES (POS) CGA YES CGG YES CAT YES HISTIDINE 2 CACYES TAA YES STOP CODON 3 STOP SIGNAL 3 TAG YES (STP) TGA YES TOTAL 32 10Amino Acids Are Represented NPL: POL: NEG: POS: STP = 13: 10: 0: 6: 3

TABLE 51 Mutagenic Cassette: G/T, N, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 4 NONPOLAR 17 GGC YES(NPL) GGA YES GGG YES GCT YES ALANINE 4 GCC YES GCA YES GCG YES GTT YESVALINE 4 GTC YES GTA YES GTG YES TTA YES LEUCINE 2 TTG YES ISOLEUCINE 0METHIONINE 0 TTT YES PHENYLALANINE 2 TTC YES TGG YES TRYPTOPHAN 1PROLINE 0 TCT YES SERINE 4 POLAR 8 TCC YES NONIONIZABLE TCA YES (POL)TCG YES TGT YES CYSTEINE 2 TGC YES ASPARAGINE 0 GLUTAMINE 0 TAT YESTYROSINE 2 TAC YES THREONINE 0 GAT YES ASPARTIC ACID 2 IONIZABLE: ACIDIC4 GAC YES NEGATIVE CHARGE GAA YES GLUTAMIC ACID 2 (NEG) GAG YES LYSINE 0IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0 (POS) TAA YESSTOP CODON 3 STOP SIGNAL 3 TAG YES (STP) TGA YES TOTAL 32 11 Amino AcidsAre Represented NPL: POL: NEG: POS: STP = 17: 8: 4: 0: 3

TABLE 52 Mutagenic Cassette: N, A, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 0 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 PROLINE 0 SERINE 0 POLAR 6 CYSTEINE 0 NONIONIZABLE AAT YES ASPARAGINE2 (POL) AAC YES CAA YES GLUTAMINE 2 CAG YES TAT YES TYROSINE 2 TAC YESTHREONINE 0 GAT YES ASPARTIC ACID 2 IONIZABLE: ACIDIC 4 GAC YES NEGATIVECHARGE GAA YES GLUTAMIC ACID 2 (NEG) GAG YES AAA YES LYSINE 2 IONIZABLE:BASIC 4 AAG YES POSITIVE CHARGE ARGININE 0 (POS) CAT YES HISTIDINE 2 CACYES TAA YES STOP CODON 2 STOP SIGNAL 2 TAG YES (STP) TOTAL 16 7 AminoAcids Are Represented NPL: POL: NEG: POS: STP = 0: 6: 4: 4: 2

TABLE 53 Mutagenic Cassette: N, C, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 8 GCT YES ALANINE 4(NPL) GCC YES GCA YES GCG YES VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE0 PHENYLALANINE 0 TRYPTOPHAN 0 CCT YES PROLINE 4 CCC YES CCA YES CCG YESTCT YES SERINE 4 POLAR 8 TCC YES NONIONIZABLE TCA YES (POL) TCG YESCYSTEINE 0 ASPARAGINE 0 GLUTAMINE 0 TYROSINE 0 ACT YES THREONINE 4 ACCYES ACA YES ACG YES ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0NEGATIVE CHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVECHARGE HISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 16 4Amino Acids Are Represented NPL: POL: NEG: POS: STP = 8: 8: 0: 0: 0

TABLE 54 Mutagenic Cassette: N, G, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 4 NONPOLAR 5 GGC YES(NPL) GGA YES GGG YES ALANINE 0 VALINE 0 LEUCINE 0 ISOLEUCINE 0METHIONINE 0 PHENYLALANINE 0 TGG YES TRYPTOPHAN 1 PROLINE 0 AGT YESSERINE 2 POLAR 4 AGC YES NONIONIZABLE TGT YES CYSTEINE 2 (POL) TGC YESASPARAGINE 0 GLUTAMINE 0 TYROSINE 0 THREONINE 0 ASPARTIC ACID 0IONIZABLE ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE 0IONIZABLE: BASIC 6 CGT YES ARGININE 6 POSITIVE CHARGE CGC YES (POS) CGAYES CGG YES AGA YES AGC YES HISTIDINE 0 TGA YES STOP CODON 1 STOP SIGNAL1 (STP) TOTAL 16 5 Amino Acids Are Represented NPL: POL: NEG: POS: STP =5: 4: 0: 6: 1

TABLE 55 Mutagenic Cassette: N, T, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 16 ALANINE 0 (NPL)GTT YES VALINE 4 GTC YES GTA YES GTG YES TTA YES LEUCINE 6 TTG YES CTTYES CTC YES CTA YES CTG YES ATT YES ISOLEUCINE 3 ATC YES ATA YES ATG YESMETHIONINE 1 TTT YES PHENYLALANINE 2 TTC YES TRYPTOPHAN 0 PROLINE 0SERINE 0 POLAR 0 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0TYROSINE 0 THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID0 NEGATIVE CHARGE (NEG) LYSINE 0 IONIZABLE. BASIC 0 ARGININE 0 POSITIVECHARGE HISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 16 5Amino Acids Are Represented NPL: POL: NEG: POS: STP = 16: 0: 0: 0: 0

TABLE 56 Mutagenic Cassette: N, A/C, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 8 GCT YES ALANINE 4(NPL) GCC YES GCA YES GCG YES VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE0 PHENYLALANINE 0 TRYPTOPHAN 0 CCT YES PROLINE 4 CCC YES CCA YES CCG YESTCT YES SERINE 4 POLAR 14 TCC YES NONIONIZABLE TCA YES (POL) TCG YESCYSTEINE 0 AAT YES ASPARAGINE 2 AAC YES CAA YES GLUTAMINE 2 CAG YES TATYES TYROSINE 2 TAC YES ACT YES THREONINE 4 ACC YES ACA YES ACG YES GATYES ASPARTIC ACID 2 IONIZABLE: ACIDIC 4 GAC YES NEGATIVE CHARGE GAA YESGLUTAMIC ACID 2 (NEG) GAG YES AAA YES LYSINE 2 IONIZABLE: BASIC 4 AAGYES POSITIVE CHARGE ARGININE 0 (POS) CAT YES HISTIDINE 2 CAC YES TAA YESSTOP CODON 2 STOP SIGNAL 2 TAG YES (STP) TOTAL 32 11 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 8: 14: 4: 4: 2

TABLE 57 Mutagenic Cassette: N, A/G, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 4 NONPOLAR 5 GGC YES(NPL) GGA YES GGG YES ALANINE 0 VALINE 0 LEUCINE 0 ISOLEUCINE 0METHIONINE 0 PHENYLALANINE 0 TGG YES TRYPTOPHAN 1 PROLINE 0 AGT YESSERINE 2 POLAR 10 AGC YES NONIONIZABLE TGT YES CYSTEINE 2 (POL) TGC YESAAT YES ASPARAGINE 2 AAC YES CAA YES GLUTAMINE 2 CAG YES TAT YESTYROSINE 2 TAC YES THREONINE 0 GAT YES ASPARTIC ACID 2 IONIZABLE: ACIDIC4 GAC YES NEGATIVE CHARGE GAA YES GLUTAMIC ACID 2 (NEG) GAG YES AAA YESLYSINE 2 IONIZABLE: BASIC 10 AAG YES POSITIVE CHARGE CGT YES ARGININE 6(POS) CGC YES CGA YES CGG YES AGA YES AGG YES CAT YES HISTIDINE 2 CACYES TAA YES STOP CODON 3 STOP SIGNAL 3 TAG YES (STP) TGA YES TOTAL 32 12Amino Acids Are Represented NPL: POL: NEG: POS: STP = 5: 10: 4: 10: 3

TABLE 58 Mutagenic Cassette: N, A/T, N CODON Represented CATEGORY(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 16 ALANINE 0 (NPL)GTT YES VALINE 4 GTC YES GTA YES GTG YES TTA YES LEUCINE 6 TTG YES CTTYES CTC YES CTA YES CTG YES ATT YES ISOLEUCINE 3 ATC YES ATA YES ATG YESMETHIONINE 1 TTT YES PHENYLALANINE 2 TTC YES TRYPTOPHAN 0 PROLINE 0SERINE 0 POLAR 6 CYSTEINE 0 NONIONIZABLE AAT YES ASPARAGINE 2 (POL) AACYES CAA YES GLUTAMINE 2 CAG YES TAT YES TYROSINE 2 TAC YES THREONINE 0GAT YES ASPARTIC ACID 2 IONIZABLE: ACIDIC 4 GAC YES NEGATIVE CHARGE GAAYES GLUTAMIC ACID 2 (NEG) GAG YES AAA YES LYSINE 2 IONIZABLE: BASIC 4AAG YES POSITIVE CHARGE ARGININE 0 (POS) CAT YES HISTIDINE 2 CAC YES TAAYES STOP CODON 2 STOP SIGNAL 2 TAG YES (STP) TOTAL 32 12 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 16: 6: 4: 4: 2

TABLE 59 Mutagenic Cassette: N, C/G, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 4 NONPOLAR 13 GGC YES(NPL) GGA YES GGG YES GCT YES ALANINE 4 GCC YES GCA YES GCG YES VALINE 0LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TGG YES TRYPTOPHAN 1CCT YES PROLINE 4 CCC YES CCA YES CCG YES TCT YES SERINE 6 POLAR 12 TCCYES NONIONIZABLE TCA YES (POL) TCG YES AGT YES AGC YES TGT YES CYSTEINE2 TGC YES ASPARAGINE 0 GLUTAMINE 0 TYROSINE 0 ACT YES THREONINE 4 ACCYES ACA YES ACG YES ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0NEGATIVE CHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 6 CGT YES ARGININE 6POSITIVE CHARGE CGC YES (POS) CGA YES CGG YES AGA YES AGG YES HISTIDINE0 TGA YES STOP CODON 1 STOP SIGNAL 1 (STP) 32 8 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 13: 12: 0: 6: 1

TABLE 60 Mutagenic Cassette: N, C/T, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 24 GCT YES ALANINE 4(NPL) GCC YES GCA YES GCG YES GTT YES VALINE 4 GTC YES GTA YES GTG YESTTA YES LEUCINE 6 TTG YES CTT YES CTC YES CTA YES CTG YES ATT YESISOLEUCINE 3 ATC YES ATA YES ATG YES METHIONINE 1 TTT YES PHENYLALANINE2 TTC YES TRYPTOPHAN 0 CCT YES PROLINE 4 CCC YES CCA YES CCG YES TCT YESSERINE 4 POLAR 8 TCC YES NONIONIZABLE TCA YES (POL) TCG YES CYSTEINE 0ASPARAGINE 0 GLUTAMINE 0 TYROSINE 0 ACT YES THREONINE 4 ACC YES ACA YESACG YES ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVECHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGEHISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 32 9 AminoAcids Are Represented NPL: POL: NEG: POS: STP = 24: 8: 0: 0: 0

TABLE 61 Mutagenic Cassette: N, G/T, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 4 NONPOLAR 21 GGC YES(NPL) GGA YES GGG YES ALANINE 0 GTT YES VALINE 4 GTC YES GTA YES GTG YESTTA YES LEUCINE 6 TTG YES CTT YES CTC YES CTA YES CTG YES ATT YESISOLEUCINE 3 ATC YES ATA YES ATG YES METHIONINE 1 TTT YES PHENYLALANINE2 TTC YES TGG YES TRYPTOPHAN 1 PROLINE 0 AGT YES SERINE 2 POLAR 4 AGCYES NONIONIZABLE TGT YES CYSTEINE 2 (POL) TGC YES ASPARAGINE 0 GLUTAMINE0 TYROSINE 0 THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMICACID 0 NEGATIVE CHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 6 CGT YESARGININE 6 POSITIVE CHARGE CGC YES (POS) CGA YES CGG YES AGA YES AGG YESHISTIDINE 0 TGA YES STOP CODON 1 STOP SIGNAL 1 (STP) TOTAL 32 10 AminoAcids Are Represented NPL: POL: NEG: POS: STP = 21: 4: 0: 6: 1

TABLE 62 Mutagenic Cassette: N, A/C/G, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 4 NONPOLAR 13 GGC YES(NPL) GGA YES GGG YES GCT YES ALANINE 4 GCC YES GCA YES GCG YES VALINE 0LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TGG YES TRYPTOPHAN 1CCT YES PROLINE 4 CCC YES CCA YES CCG YES TCT YES SERINE 6 POLAR 18 TCCYES NONIONIZABLE TCA YES (POL) TCG YES AGT YES AGC YES TGT YES CYSTEINE2 TGC YES AAT YES ASPARAGINE 2 AAC YES CAA YES GLUTAMINE 2 CAG YES TATYES TYROSINE 2 TAC YES ACT YES THREONINE 4 ACC YES ACA YES ACG YES GATYES ASPARTIC ACID 2 IONIZABLE: ACIDIC 4 GAC YES NEGATIVE CHARGE GAA YESGLUTAMIC ACID 2 (NEG) GAG YES AAA YES LYSINE 2 IONIZABLE: BASIC 10 AAGYES POSITIVE CHARGE CGT YES ARGININE 6 (POS) CGC YES CGA YES CGG YES AGAYES AGG YES CAT YES HISTIDINE 2 CAC YES TAA YES STOP CODON 3 STOP SIGNAL3 TAG YES (STP) TGA YES TOTAL 48 15 Amino Acids Are Represented NPL:POL: NEG: POS: STP = 13: 18: 4: 10: 3

TABLE 63 Mutagenic Cassette: N, A/C/T, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 24 GCT YES ALANINE 4(NPL) GCC YES GCA YES GCG YES GTT YES VALINE 4 GTC YES GTA YES GTG YESTTA YES LEUCINE 6 TTG YES CTT YES CTC YES CTA YES CTG YES ATT YESISOLEUCINE 3 ATC YES ATA YES ATG YES METHIONINE 1 TTT YES PHENYLALANINE2 TTC YES TRYPTOPHAN 0 CCT YES PROLINE 4 CCC YES CCA YES CCG YES TCT YESSERINE 4 POLAR 14 TCC YES NONIONIZABLE TCA YES (POL) TCG YES CYSTEINE 0AAT YES ASPARAGINE 2 AAC YES CAA YES GLUTAMINE 2 CAG YES TAT YESTYROSINE 2 TAC YES ACT YES THREONINE 4 ACC YES ACA YES ACG YES GAT YESASPARTIC ACID 2 IONIZABLE: ACIDIC 4 GAC YES NEGATIVE CHARGE GAA YESGLUTAMIC ACID 2 (NEG) GAG YES AAA YES LYSINE 2 IONIZABLE: BASIC 4 AAGYES POSITIVE CHARGE ARGININE 0 (POS) CAT YES HISTIDINE 2 CAC YES TAA YESSTOP CODON 2 STOP SIGNAL 2 TAG YES (STP) TOTAL 48 16 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 24: 14: 4: 4: 2

TABLE 64 Mutagenic Cassette: N, A/G/T, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 4 NONPOLAR 21 GGC YES(NPL) GGA YES GGG YES ALANINE 0 GTT YES VALINE 4 GTC YES GTA YES GTG YESTTA YES LEUCINE 6 TTG YES CTT YES CTC YES CTA YES CTG YES ATT YESISOLEUCINE 3 ATC YES ATA YES ATG YES METHIONINE 1 TTT YES PHENYLALANINE2 TTC YES TGG YES TRYPTOPHAN 1 PROLINE 0 AGT YES SERINE 2 POLAR 10 AGCYES NONIONIZABLE TGT YES CYSTEINE 2 (POL) TGC YES AAT YES ASPARAGINE 2AAC YES CAA YES GLUTAMINE 2 CAG YES TAT YES TYROSINE 2 TAC YES THREONINE0 GAT YES ASPARTIC ACID 2 IONIZABLE: ACIDIC 4 GAC YES NEGATIVE CHARGEGAA YES GLUTAMIC ACID 2 (NEG) GAG YES AAA YES LYSINE 2 IONIZABLE: BASIC10 AAG YES POSITIVE CHARGE CGT YES ARGININE 6 (POS) CGC YES CGA YES CGGYES AGA YES AGG YES CAT YES HISTIDINE 2 CAC YES TAA YES STOP CODON 3STOP SIGNAL 3 TAG YES (STP) TGA YES TOTAL 48 17 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 21: 10: 4: 10: 3

TABLE 65 Mutagenic Cassette: N, C/G/T, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 4 NONPOLAR 29 GGC YES(NPL) GGA YES GGG YES GCT YES ALANINE 4 GCC YES GCA YES GCG YES GTT YESVALINE 4 GTC YES GTA YES GTG YES TTA YES LEUCINE 6 TTG YES CTT YES CTCYES CTA YES CTG YES ATT YES ISOLEUCINE 3 ATC YES ATA YES ATG YESMETHIONINE 1 TTT YES PHENYLALANINE 2 TTC YES TGG YES TRYPTOPHAN 1 CCTYES PROLINE 4 CCC YES CCA YES CCG YES TCT YES SERINE 6 POLAR 12 TCC YESNONIONIZABLE TCA YES (POL) TCG YES AGT YES AGC YES TGT YES CYSTEINE 2TGC YES ASPARAGINE 0 GLUTAMINE 0 TYROSINE 0 ACT YES THREONINE 4 ACC YESACA YES ACG YES ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0NEGATIVE CHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 6 CGT YES ARGININE 6POSITIVE CHARGE CGC YES (POS) CGA YES CGG YES AGA YES AGG YES HISTIDINE0 TGA YES STOP CODON 1 STOP SIGNAL 1 (STP) TOTAL 48 13 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 29: 12: 0: 6: 1

TABLE 66 Mutagenic Cassette: C, C, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 4 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 CCT YES PROLINE 4 CCC YES CCA YES CCG YES SERINE 0 POLAR 0 CYSTEINE 0NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0 THREONINE 0ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0(POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 1 Amino Acid IsRepresented NPL: POL: NEG: POS: STP = 4: 0: 0: 0: 0

TABLE 67 Mutagenic Cassette: G, G, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 4 NONPOLAR 4 GGC YES(NPL) GGA YES GGG YES ALANINE 0 VALINE 0 LEUCINE 0 ISOLEUCINE 0METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 0CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVECHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGEHISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 1 Amino AcidIs Represented NPL: POL: NEG: POS: STP = 0 4: 0: 0: 0: 0

TABLE 68 Mutagenic Cassette: G, C, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 4 GCT YES ALANINE 4(NPL) GCC YES GCA YES GCG YES VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE0 PHENYLALANINE 0 TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 0 CYSTEINE 0NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0 THREONINE 0ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0(POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 1 Amino Acid IsRepresented NPL: POL: NEG: POS: STP = 4: 0: 0: 0: 0

TABLE 69 Mutagenic Cassette: G, T, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 4 ALANINE 0 (NPL)GTT YES VALINE 4 GTC YES GTA YES GTG YES LEUCINE 0 ISOLEUCINE 0METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 0CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVECHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGEHISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 1 Amino AcidIs Represented NPL: POL: NEG: POS: STP = 4: 0: 0: 0: 0

TABLE 70 Mutagenic Cassette: C, G, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 0 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 PROLINE 0 SERINE 0 POLAR 0 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL)GLUTAMINE 0 TYROSINE 0 THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 4 CGTYES ARGININE 4 POSITIVE CHARGE CGC YES (POS) CGA YES CGG YES HISTIDINE 0STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 1 Amino Acid Is RepresentedNPL: POL: NEG: POS: STP = 0: 0: 0: 4: 0

TABLE 71 Mutagenic Cassette: C, T, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 4 ALANINE 0 (NPL)VALINE 0 CTT YES LEUCINE 4 CTC YES CTA YES CTG YES ISOLEUCINE 0METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 0CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVECHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGEHISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 1 Amino AcidIs Represented NPL: POL: NEG: POS: STP = 4: 0: 0: 0: 0

TABLE 72 Mutagenic Cassette: T, C, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 0 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 PROLINE 0 TCT YES SERINE 4 POLAR 4 TCC YES NONIONIZABLE TCA YES (POL)TCG YES CYSTEINE 0 ASPARAGINE 0 GLUTAMINE 0 TYROSINE 0 THREONINE 0ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0(POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 1 Amino Acid IsRepresented NPL: POL: NEG: POS: STP = 0: 4: 0: 0: 0

TABLE 73 Mutagenic Cassette: A, C, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 0 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 PROLINE 0 SERINE 0 POLAR 4 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL)GLUTAMINE 0 TYROSINE 0 ACT YES THREONINE 4 ACC YES ACA YES ACG YESASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE(NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0(POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 1 Amino Acid IsRepresented NPL: POL: NEG: POS: STP = 0: 4: 0: 0: 0

TABLE 74 Mutagenic Cassette: G, A, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 0 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 PROLINE 0 SERINE 0 POLAR 0 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL)GLUTAMINE 0 TYROSINE 0 THREONINE 0 GAT YES ASPARTIC ACID 2 IONIZABLE:ACIDIC 4 GAC YES NEGATIVE CHARGE GAA YES GLUTAMIC ACID 2 (NEG) GAG YESLYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0 (POS)STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 2 Amino Acids Are RepresentedNPL: POL: NEG: POS: STP = 0: 0: 4: 0: 0

TABLE 75 Mutagenic Cassette: A, T, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 4 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ATT YES ISOLEUCINE 3 ATC YES ATA YES ATG YESMETHIONINE 1 PHENYLALANINE 0 TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 0CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVECHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGEHISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 2 Amino AcidsAre Represented NPL: POL: NEG: POS: STP = 4: 0: 0: 0: 0

TABLE 76 Mutagenic Cassette: C, A, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 0 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 PROLINE 0 SERINE 0 POLAR 2 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL)CAA YES GLUTAMINE 2 CAG YES TYROSINE 0 THREONINE 0 ASPARTIC ACID 0IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE 0IONIZABLE: BASIC 2 ARGININE 0 POSITIVE CHARGE CAT YES HISTIDINE 2 (POS)CAC YES STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 2 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 0: 2: 0: 2: 0

TABLE 77 Mutagenic Cassette: T, T, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 4 ALANINE 0 (NPL)VALINE 0 TTA YES LEUCINE 2 TTG YES ISOLEUCINE 0 METHIONINE 0 TTT YESPHENYLALANINE 2 TTC YES TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 0 CYSTEINE0 NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 0 THREONINE 0 ASPARTICACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0 (POS) STOPCODON 0 STOP SIGNAL 0 (STP) TOTAL 4 2 Amino Acids Are Represented NPL:POL: NEG: POS: STP = 4: 0: 0: 0: 0

TABLE 78 Mutagenic Cassette: A, A, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 0 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 PROLINE 0 SERINE 0 POLAR 2 CYSTEINE 0 NONIONIZABLE AAT YES ASPARAGINE2 (POL) AAC YES GLUTAMINE 0 TYROSINE 0 THREONINE 0 ASPARTIC ACID 0IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) AAA YES LYSINE2 IONIZABLE: BASIC 2 AAG YES POSITIVE CHARGE ARGININE 0 (POS) HISTIDINE0 STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 2 Amino Acids Are RepresentedNPL: POL: NEG: POS: STP = 0: 2: 0: 2: 0

TABLE 79 Mutagenic Cassette: T, A, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 0 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 PROLINE 0 SERINE 0 POLAR 2 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL)GLUTAMINE 0 TAT YES TYROSINE 2 TAC YES THREONINE 0 ASPARTIC ACID 0IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE 0IONIZABLE: BASIC 0 ARGININE 0 POSITIVE CHARGE HISTIDINE 0 (POS) TAA YESSTOP CODON 2 STOP SIGNAL 2 TAG YES (STP) TOTAL 4 1 Amino Acid IsRepresented NPL: POL: NEG: POS: STP = 0: 2: 0: 0: 2

TABLE 80 Mutagenic Cassette: T, G, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 1 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TGG YESTRYPTOPHAN 1 PROLINE 0 SERINE 0 POLAR 2 TGT YES CYSTEINE 2 NONIONIZABLETGC YES (POL) TYROSINE 0 THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 0ARGININE 0 POSITIVE CHARGE (POS) HISTIDINE 0 TGA YES STOP CODON 1 STOPSIGNAL 1 (STP) TOTAL 4 2 Amino Acids Are Represented NPL: POL: NEG: POS:STP = 1: 2: 0: 0: 1

TABLE 81 Mutagenic Cassette: A, G, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 0 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 PROLINE 0 AGT YES SERINE 2 POLAR 2 AGC YES NONIONIZABLE CYSTEINE 0(POL) ASPARAGINE 0 GLUTAMINE 0 TYROSINE 0 THREONINE 0 ASPARTIC ACID 0IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE 0IONIZABLE: BASIC 2 AGA YES ARGININE 2 POSITIVE CHARGE AGG YES (POS)HISTIDINE 0 STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 4 2 Amino Acids AreRepresented NPL: POL: NEG: POS: STP = 0: 2: 0: 2: 0

TABLE 82 Mutagenic Cassette: G/C, G, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GGT YES GLYCINE 4 NONPOLAR 4 GGC YES(NPL) GGA YES GGG YES ALANINE 0 VALINE 0 LEUCINE 0 ISOLEUCINE 0METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN 0 PROLINE 0 SERINE 0 POLAR 0CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0 TYROSINE 0THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID 0 NEGATIVECHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 4 CGT YES ARGININE 4 POSITIVECHARGE CGC YES (POS) CGA YES CGG YES HISTIDINE 0 STOP CODON 0 STOPSIGNAL 0 (STP) TOTAL 8 2 Amino Acids Are Represented NPL: POL: NEG: POS:STP = 4: 0: 0: 4: 0

TABLE 83 Mutagenic Cassette: G/C, C, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 8 GCT YES ALANINE 4(NPL) GCC YES GCA YES GCG YES VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE0 PHENYLALANINE 0 TRYPTOPHAN 0 CCT YES PROLINE 4 CCC YES CCA YES CCG YESSERINE 0 POLAR 0 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL) GLUTAMINE 0TYROSINE 0 THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0 GLUTAMIC ACID0 NEGATIVE CHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 0 ARGININE 0 POSITIVECHARGE HISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 8 2Amino Acids Are Represented NPL: POL: NEG: POS: STP = 8: 0: 0: 0: 0

TABLE 84 Mutagenic Cassette: G/C, A, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 0 ALANINE 0 (NPL)VALINE 0 LEUCINE 0 ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN0 PROLINE 0 SERINE 0 POLAR 2 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL)CAA YES GLUTAMINE 2 CAG YES TYROSINE 0 THREONINE 0 GAT YES ASPARTIC ACID2 IONIZABLE: ACIDIC 4 GAC YES NEGATIVE CHARGE GAA YES GLUTAMIC ACID 2(NEG) GAG YES LYSINE 0 IONIZABLE: BASIC 2 ARGININE 0 POSITIVE CHARGE CATYES HISTIDINE 2 (POS) CAC YES STOP CODON 0 STOP SIGNAL 0 (STP) TOTAL 8 4Amino Acids Are Represented NPL: POL: NEG: POS: STP = 0: 2: 4: 2: 0

TABLE 85 Mutagenic Cassette: G/C, T, N CODON Represented AMINO ACID(Frequency) CATEGORY (Frequency) GLYCINE 0 NONPOLAR 8 ALANINE 0 (NPL)GTT YES VALINE 4 GTC YES GTA YES GTG YES CTT YES LEUCINE 4 CTC YES CTAYES CTG YES ISOLEUCINE 0 METHIONINE 0 PHENYLALANINE 0 TRYPTOPHAN 0PROLINE 0 SERINE 0 POLAR 0 CYSTEINE 0 NONIONIZABLE ASPARAGINE 0 (POL)GLUTAMINE 0 TYROSINE 0 THREONINE 0 ASPARTIC ACID 0 IONIZABLE: ACIDIC 0GLUTAMIC ACID 0 NEGATIVE CHARGE (NEG) LYSINE 0 IONIZABLE: BASIC 0ARGININE 0 POSITIVE CHARGE HISTIDINE 0 (POS) STOP CODON 0 STOP SIGNAL 0(STP) TOTAL 8 2 Amino Acids Are Represented NPL: POL: NEG: POS: STP = 8:0: 0: 0: 0

2.11.2. Chimerizations

2.11.2.1 “Shuffling”

Nucleic acid shuffling is a method for in vitro or in vivo homologousrecombination of pools of shorter or smaller polynucleotides to producea polynucleotide or polynucleotides. Mixtures of related nucleic acidsequences or polynucleotides are subjected to sexual PCR to providerandom polynucleotides, and reassembled to yield a library or mixedpopulation of recombinant hybrid nucleic acid molecules orpolynucleotides.

In contrast to cassette mutagenesis, only shuffling and error-prone PCRallow one to mutate a pool of sequences blindly (without sequenceinformation other than primers).

The advantage of the mutagenic shuffling of this invention overerror-prone PCR alone for repeated selection can best be explained withan example from antibody engineering. Consider DNA shuffling as comparedwith error-prone PCR (not sexual PCR). The initial library of selectedpooled sequences can consist of related sequences of diverse origin(i.e. antibodies from naive mRNA) or can be derived by any type ofmutagenesis (including shuffling) of a single antibody gene. Acollection of selected complementarity determining regions (“CDRs”) isobtained after the first round of affinity selection. In the diagram thethick CDRs confer onto the antibody molecule increased affinity for theantigen. Shuffling allows the free combinatorial association of all ofthe CDR1s with all of the CDR2s with all of the CDR3s, for example.

This method differs from error-prone PCR, in that it is an inverse chainreaction. In error-prone PCR, the number of polymerase start sites andthe number of molecules grows exponentially. However, the sequence ofthe polymerase start sites and the sequence of the molecules remainsessentially the same. In contrast, in nucleic acid reassembly orshuffling of random polynucleotides the number of start sites and thenumber (but not size) of the random polynucleotides decreases over time.For polynucleotides derived from whole plasmids the theoretical endpointis a single, large concatemeric molecule.

Since cross-overs occur at regions of homology, recombination willprimarily occur between members of the same sequence family. Thisdiscourages combinations of CDRs that are grossly incompatible (e.g.,directed against different epitopes of the same antigen). It iscontemplated that multiple families of sequences can be shuffled in thesame reaction. Further, shuffling generally conserves the relativeorder, such that, for example, CDR1 will not be found in the position ofCDR2.

Rare shufflants will contain a large number of the best (eg. highestaffinity) CDRs and these rare shufflants may be selected based on theirsuperior affinity.

CDRs from a pool of 100 different selected antibody sequences can bepermutated in up to 1006 different ways. This large number ofpermutations cannot be represented in a single library of DNA sequences.Accordingly, it is contemplated that multiple cycles of DNA shufflingand selection may be required depending on the length of the sequenceand the sequence diversity desired.

Error-prone PCR, in contrast, keeps all the selected CDRs in the samerelative sequence, generating a much smaller mutant cloud.

The template polynucleotide which may be used in the methods of thisinvention may be DNA or RNA. It may be of various lengths depending onthe size of the gene or shorter or smaller polynucleotide to berecombined or reassembled. Preferably, the template polynucleotide isfrom 50 bp to 50 kb. It is contemplated that entire vectors containingthe nucleic acid encoding the protein of interest can be used in themethods of this invention, and in fact have been successfully used.

The template polynucleotide may be obtained by amplification using thePCR reaction (U.S. Pat. No. 4,683,202 and U.S. Pat. No. 4,683,195) orother amplification or cloning methods. However, the removal of freeprimers from the PCR products before subjecting them to pooling of thePCR products and sexual PCR may provide more efficient results. Failureto adequately remove the primers from the original pool before sexualPCR can lead to a low frequency of crossover clones.

The template polynucleotide often should be double-stranded. Adouble-stranded nucleic acid molecule is recommended to ensure thatregions of the resulting single-stranded polynucleotides arecomplementary to each other and thus can hybridize to form adouble-stranded molecule.

It is contemplated that single-stranded or double-stranded nucleic acidpolynucleotides having regions of identity to the templatepolynucleotide and regions of heterology to the template polynucleotidemay be added to the template polynucleotide, at this step. It is alsocontemplated that two different but related polynucleotide templates canbe mixed at this step.

The double-stranded polynucleotide template and any added double- orsingle-stranded polynucleotides are subjected to sexual PCR whichincludes slowing or halting to provide a mixture of from about 5 bp to 5kb or more. Preferably the size of the random polynucleotides is fromabout 10 bp to 1000 bp, more preferably the size of the polynucleotidesis from about 20 bp to 500 bp.

Alternatively, it is also contemplated that double-stranded nucleic acidhaving multiple nicks may be used in the methods of this invention. Anick is a break in one strand of the double-stranded nucleic acid. Thedistance between such nicks is preferably 5 bp to 5 kb, more preferablybetween 10 bp to 1000 bp. This can provide areas of self-priming toproduce shorter or smaller polynucleotides to be included with thepolynucleotides resulting from random primers, for example.

The concentration of any one specific polynucleotide will not be greaterthan 1% by weight of the total polynucleotides, more preferably theconcentration of any one specific nucleic acid sequence will not begreater than 0.1% by weight of the total nucleic acid.

The number of different specific polynucleotides in the mixture will beat least about 100, preferably at least about 500, and more preferablyat least about 1000.

At this step single-stranded or double-stranded polynucleotides, eithersynthetic or natural, may be added to the random double-stranded shorteror smaller polynucleotides in order to increase the heterogeneity of themixture of polynucleotides.

It is also contemplated that populations of double-stranded randomlybroken polynucleotides may be mixed or combined at this step with thepolynucleotides from the sexual PCR process and optionally subjected toone or more additional sexual PCR cycles.

Where insertion of mutations into the template polynucleotide isdesired, single-stranded or double-stranded polynucleotides having aregion of identity to the template polynucleotide and a region ofheterology to the template polynucleotide may be added in a 20 foldexcess by weight as compared to the total nucleic acid, more preferablythe single-stranded polynucleotides may be added in a 10 fold excess byweight as compared to the total nucleic acid.

Where a mixture of different but related template polynucleotides isdesired, populations of polynucleotides from each of the templates maybe combined at a ratio of less than about 1:100, more preferably theratio is less than about 1:40. For example, a backcross of the wild-typepolynucleotide with a population of mutated polynucleotide may bedesired to eliminate neutral mutations (e.g., mutations yielding aninsubstantial alteration in the phenotypic property being selected for).In such an example, the ratio of randomly provided wild-typepolynucleotides which may be added to the randomly provided sexual PCRcycle hybrid polynucleotides is approximately 1:1 to about 100:1, andmore preferably from 1:1 to 40:1.

The mixed population of random polynucleotides are denatured to formsingle-stranded polynucleotides and then re-annealed. Only thosesingle-stranded polynucleotides having regions of homology with othersingle-stranded polynucleotides will re-anneal.

The random polynucleotides may be denatured by heating. One skilled inthe art could determine the conditions necessary to completely denaturethe double-stranded nucleic acid. Preferably the temperature is from 80°C. to 100° C., more preferably the temperature is from 90° C. to 96° C.other methods which may be used to denature the polynucleotides includepressure (36) and pH.

The polynucleotides may be re-annealed by cooling. Preferably thetemperature is from 20° C. to 75° C., more preferably the temperature isfrom 40° C. to 65° C. If a high frequency of crossovers is needed basedon an average of only 4 consecutive bases of homology, recombination canbe forced by using a low annealing temperature, although the processbecomes more difficult. The degree of renaturation which occurs willdepend on the degree of homology between the population ofsingle-stranded polynucleotides.

Renaturation can be accelerated by the addition of polyethylene glycol(“PEG”) or salt. The salt concentration is preferably from 0 mM to 200mM, more preferably the salt concentration is from 10 mM to 100 mm. Thesalt may be KCl or NaCl. The concentration of PEG is preferably from 0%to 20%, more preferably from 5% to 10%.

The annealed polynucleotides are next incubated in the presence of anucleic acid polymerase and dNTP's (i.e. dATP, dCTP, dGTP and dTTP). Thenucleic acid polymerase may be the Klenow fragment, the Taq polymeraseor any other DNA polymerase known in the art.

The approach to be used for the assembly depends on the minimum degreeof homology that should still yield crossovers. If the areas of identityare large, Taq polymerase can be used with an annealing temperature ofbetween 45-65° C. If the areas of identity are small, Klenow polymerasecan be used with an annealing temperature of between 20-30° C. Oneskilled in the art could vary the temperature of annealing to increasethe number of cross-overs achieved.

The polymerase may be added to the random polynucleotides prior toannealing, simultaneously with annealing or after annealing.

The cycle of denaturation, renaturation and incubation in the presenceof polymerase is referred to herein as shuffling or reassembly of thenucleic acid. This cycle is repeated for a desired number of times.Preferably the cycle is repeated from 2 to 50 times, more preferably thesequence is repeated from 10 to 40 times.

The resulting nucleic acid is a larger double-stranded polynucleotide offrom about 50 bp to about 100 kb, preferably the larger polynucleotideis from 500 bp to 50 kb.

This larger polynucleotide may contain a number of copies of apolynucleotide having the same size as the template polynucleotide intandem. This concatemeric polynucleotide is then denatured into singlecopies of the template polynucleotide. The result will be a populationof polynucleotides of approximately the same size as the templatepolynucleotide. The population will be a mixed population where singleor double-stranded polynucleotides having an area of identity and anarea of heterology have been added to the template polynucleotide priorto shuffling. These polynucleotides are then cloned into the appropriatevector and the ligation mixture used to transform bacteria.

It is contemplated that the single polynucleotides may be obtained fromthe larger concatemeric polynucleotide by amplification of the singlepolynucleotide prior to cloning by a variety of methods including PCR(U.S. Pat. No. 4,683,195 and U.S. Pat. No. 4,683,202), rather than bydigestion of the concatemer.

The vector used for cloning is not critical provided that it will accepta polynucleotide of the desired size. If expression of the particularpolynucleotide is desired, the cloning vehicle should further comprisetranscription and translation signals next to the site of insertion ofthe polynucleotide to allow expression of the polynucleotide in the hostcell. Preferred vectors include the pUC series and the pBR series ofplasmids.

The resulting bacterial population will include a number of recombinantpolynucleotides having random mutations. This mixed population may betested to identify the desired recombinant polynucleotides. The methodof selection will depend on the polynucleotide desired.

For example, if a polynucleotide which encodes a protein with increasedbinding efficiency to a ligand is desired, the proteins expressed byeach of the portions of the polynucleotides in the population or librarymay be tested for their ability to bind to the ligand by methods knownin the art (i.e. panning, affinity chromatography). If a polynucleotidewhich encodes for a protein with increased drug resistance is desired,the proteins expressed by each of the polynucleotides in the populationor library may be tested for their ability to confer drug resistance tothe host organism. One skilled in the art, given knowledge of thedesired protein, could readily test the population to identifypolynucleotides which confer the desired properties onto the protein.

It is contemplated that one skilled in the art could use a phage displaysystem in which fragments of the protein are expressed as fusionproteins on the phage surface (Pharmacia, Milwaukee Wis.). Therecombinant DNA molecules are cloned into the phage DNA at a site whichresults in the transcription of a fusion protein a portion of which isencoded by the recombinant DNA molecule. The phage containing therecombinant nucleic acid molecule undergoes replication andtranscription in the cell. The leader sequence of the fusion proteindirects the transport of the fusion protein to the tip of the phageparticle. Thus the fusion protein which is partially encoded by therecombinant DNA molecule is displayed on the phage particle fordetection and selection by the methods described above.

It is further contemplated that a number of cycles of nucleic acidshuffling may be conducted with polynucleotides from a sub-population ofthe first population, which sub-population contains DNA encoding thedesired recombinant protein. In this manner, proteins with even higherbinding affinities or enzymatic activity could be achieved.

It is also contemplated that a number of cycles of nucleic acidshuffling may be conducted with a mixture of wild-type polynucleotidesand a sub-population of nucleic acid from the first or subsequent roundsof nucleic acid shuffling in order to remove any silent mutations fromthe sub-population.

Any source of nucleic acid, in purified form can be utilized as thestarting nucleic acid. Thus the process may employ DNA or RNA includingmessenger RNA, which DNA or RNA may be single or double stranded. Inaddition, a DNA-RNA hybrid which contains one strand of each may beutilized. The nucleic acid sequence may be of various lengths dependingon the size of the nucleic acid sequence to be mutated. Preferably thespecific nucleic acid sequence is from 50 to 50000 base pairs. It iscontemplated that entire vectors containing the nucleic acid encodingthe protein of interest may be used in the methods of this invention.

The nucleic acid may be obtained from any source, for example, fromplasmids such a pBR322, from cloned DNA or RNA or from natural DNA orRNA from any source including bacteria, yeast, viruses and higherorganisms such as plants or animals. DNA or RNA may be extracted fromblood or tissue material. The template polynucleotide may be obtained byamplification using the polynucleotide chain reaction (PCR, see U.S.Pat. No. 4,683,202 and U.S. Pat. No. 4,683,195). Alternatively, thepolynucleotide may be present in a vector present in a cell andsufficient nucleic acid may be obtained by culturing the cell andextracting the nucleic acid from the cell by methods known in the art.

Any specific nucleic acid sequence can be used to produce the populationof hybrids by the present process. It is only necessary that a smallpopulation of hybrid sequences of the specific nucleic acid sequenceexist or be created prior to the present process.

The initial small population of the specific nucleic acid sequenceshaving mutations may be created by a number of different methods.Mutations may be created by error-prone PCR. Error-prone PCR useslow-fidelity polymerization conditions to introduce a low level of pointmutations randomly over a long sequence. Alternatively, mutations can beintroduced into the template polynucleotide by oligonucleotide-directedmutagenesis. In oligonucleotide-directed mutagenesis, a short sequenceof the polynucleotide is removed from the polynucleotide usingrestriction enzyme digestion and is replaced with a syntheticpolynucleotide in which various bases have been altered from theoriginal sequence. The polynucleotide sequence can also be altered bychemical mutagenesis. Chemical mutagens include, for example, sodiumbisulfite, nitrous acid, hydroxylamine, hydrazine or formic acid. Otheragents which are analogues of nucleotide precursors includenitrosoguanidine, 5-bromouracil, 2-aminopurine, or acridine. Generally,these agents are added to the PCR reaction in place of the nucleotideprecursor thereby mutating the sequence. Intercalating agents such asproflavine, acriflavine, quinacrine and the like can also be used.Random mutagenesis of the polynucleotide sequence can also be achievedby irradiation with X-rays or ultraviolet light. Generally, plasmidpolynucleotides so mutagenized are introduced into E. coli andpropagated as a pool or library of hybrid plasmids.

Alternatively the small mixed population of specific nucleic acids maybe found in nature in that they may consist of different alleles of thesame gene or the same gene from different related species (i.e., cognategenes). Alternatively, they may be related DNA sequences found withinone species, for example, the immunoglobulin genes.

Once the mixed population of the specific nucleic acid sequences isgenerated, the polynucleotides can be used directly or inserted into anappropriate cloning vector, using techniques well-known in the art.

The choice of vector depends on the size of the polynucleotide sequenceand the host cell to be employed in the methods of this invention. Thetemplates of this invention may be plasmids, phages, cosmids, phagemids,viruses (e.g., retroviruses, parainfluenzavirus, herpesviruses,reoviruses, paramyxoviruses, and the like), or selected portions thereof(e.g., coat protein, spike glycoprotein, capsid protein). For example,cosmids and phagemids are preferred where the specific nucleic acidsequence to be mutated is larger because these vectors are able tostably propagate large polynucleotides.

If the mixed population of the specific nucleic acid sequence is clonedinto a vector it can be clonally amplified by inserting each vector intoa host cell and allowing the host cell to amplify the vector. This isreferred to as clonal amplification because while the absolute number ofnucleic acid sequences increases, the number of hybrids does notincrease. Utility can be readily determined by screening expressedpolypeptides.

The DNA shuffling method of this invention can be performed blindly on apool of unknown sequences. By adding to the reassembly mixtureoligonucleotides (with ends that are homologous to the sequences beingreassembled) any sequence mixture can be incorporated at any specificposition into another sequence mixture. Thus, it is contemplated thatmixtures of synthetic oligonucleotides, PCR polynucleotides or evenwhole genes can be mixed into another sequence library at definedpositions. The insertion of one sequence (mixture) is independent fromthe insertion of a sequence in another part of the template. Thus, thedegree of recombination, the homology required, and the diversity of thelibrary can be independently and simultaneously varied along the lengthof the reassembled DNA.

This approach of mixing two genes may be useful for the humanization ofantibodies from murine hybridomas. The approach of mixing two genes orinserting alternative sequences into genes may be useful for anytherapeutically used protein, for example, interleukin I, antibodies,tPA and growth hormone. The approach may also be useful in any nucleicacid for example, promoters or introns or 31 untranslated region or 51untranslated regions of genes to increase expression or alterspecificity of expression of proteins. The approach may also be used tomutate ribozymes or aptamers.

Shuffling requires the presence of homologous regions separating regionsof diversity. Scaffold-like protein structures may be particularlysuitable for shuffling. The conserved scaffold determines the overallfolding by self-association, while displaying relatively unrestrictedloops that mediate the specific binding. Examples of such scaffolds arethe immunoglobulin beta-barrel, and the four-helix bundle which arewell-known in the art. This shuffling can be used to createscaffold-like proteins with various combinations of mutated sequencesfor binding.

In Vitro Shuffling

The equivalents of some standard genetic matings may also be performedby shuffling in vitro. For example, a “molecular backcross” can beperformed by repeatedly mixing the hybrid's nucleic acid with thewild-type nucleic acid while selecting for the mutations of interest. Asin traditional breeding, this approach can be used to combine phenotypesfrom different sources into a background of choice. It is useful, forexample, for the removal of neutral mutations that affect unselectedcharacteristics (i.e. immunogenicity). Thus it can be useful todetermine which mutations in a protein are involved in the enhancedbiological activity and which are not, an advantage which cannot beachieved by error-prone mutagenesis or cassette mutagenesis methods.

Large, functional genes can be assembled correctly from a mixture ofsmall random polynucleotides. This reaction may be of use for thereassembly of genes from the highly fragmented DNA of fossils. Inaddition random nucleic acid fragments from fossils may be combined withpolynucleotides from similar genes from related species.

It is also contemplated that the method of this invention can be usedfor the in vitro amplification of a whole genome from a single cell asis needed for a variety of research and diagnostic applications. DNAamplification by PCR is in practice limited to a length of about 40 kb.Amplification of a whole genome such as that of E. coli (5,000 kb) byPCR would require about 250 primers yielding 125 forty kbpolynucleotides. This approach is not practical due to theunavailability of sufficient sequence data. On the other hand, randomproduction of polynucleotides of the genome with sexual PCR cycles,followed by gel purification of small polynucleotides will provide amultitude of possible primers. Use of this mix of random smallpolynucleotides as primers in a PCR reaction alone or with the wholegenome as the template should result in an inverse chain reaction withthe theoretical endpoint of a single concatamer containing many copiesof the genome. 100 fold amplification in the copy number and an averagepolynucleotide size of greater than 50 kb may be obtained when onlyrandom polynucleotides are used. It is thought that the largerconcatamer is generated by overlap of many smaller polynucleotides. Thequality of specific PCR products obtained using synthetic primers willbe indistinguishable from the product obtained from unamplified DNA. Itis expected that this approach will be useful for the mapping ofgenomes.

The polynucleotide to be shuffled can be produced as random ornon-random polynucleotides, at the discretion of the practitioner.Moreover, this invention provides a method of shuffling that isapplicable to a wide range of polynucleotide sizes and types, includingthe step of generating polynucleotide monomers to be used as buildingblocks in the reassembly of a larger polynucleotide. For example, thebuilding blocks can be fragments of genes or they can be comprised ofentire genes or gene pathways, or any combination thereof.

In Vivo Shuffling

In an embodiment of in vivo shuffling, the mixed population of thespecific nucleic acid sequence is introduced into bacterial oreukaryotic cells under conditions such that at least two differentnucleic acid sequences are present in each host cell. Thepolynucleotides can be introduced into the host cells by a variety ofdifferent methods. The host cells can be transformed with the smallerpolynucleotides using methods known in the art, for example treatmentwith calcium chloride. If the polynucleotides are inserted into a phagegenome, the host cell can be transfected with the recombinant phagegenome having the specific nucleic acid sequences. Alternatively, thenucleic acid sequences can be introduced into the host cell usingelectroporation, transfection, lipofection, biolistics, conjugation, andthe like.

In general, in this embodiment, the specific nucleic acids sequenceswill be present in vectors which are capable of stably replicating thesequence in the host cell. In addition, it is contemplated that thevectors will encode a marker gene such that host cells having the vectorcan be selected. This ensures that the mutated specific nucleic acidsequence can be recovered after introduction into the host cell.However, it is contemplated that the entire mixed population of thespecific nucleic acid sequences need not be present on a vectorsequence. Rather only a sufficient number of sequences need be clonedinto vectors to ensure that after introduction of the polynucleotidesinto the host cells each host cell contains one vector having at leastone specific nucleic acid sequence present therein. It is alsocontemplated that rather than having a subset of the population of thespecific nucleic acids sequences cloned into vectors, this subset may bealready stably integrated into the host cell.

It has been found that when two polynucleotides which have regions ofidentity are inserted into the host cells homologous recombinationoccurs between the two polynucleotides. Such recombination between thetwo mutated specific nucleic acid sequences will result in theproduction of double or triple hybrids in some situations.

It has also been found that the frequency of recombination is increasedif some of the mutated specific nucleic acid sequences are present onlinear nucleic acid molecules. Therefore, in a preferred embodiment,some of the specific nucleic acid sequences are present on linearpolynucleotides.

After transformation, the host cell transformants are placed underselection to identify those host cell transformants which containmutated specific nucleic acid sequences having the qualities desired.For example, if increased resistance to a particular drug is desiredthen the transformed host cells may be subjected to increasedconcentrations of the particular drug and those transformants producingmutated proteins able to confer increased drug resistance will beselected. If the enhanced ability of a particular protein to bind to areceptor is desired, then expression of the protein can be induced fromthe transformants and the resulting protein assayed in a ligand bindingassay by methods known in the art to identify that subset of the mutatedpopulation which shows enhanced binding to the ligand. Alternatively,the protein can be expressed in another system to ensure properprocessing.

Once a subset of the first recombined specific nucleic acid sequences(daughter sequences) having the desired characteristics are identified,they are then subject to a second round of recombination.

In the second cycle of recombination, the recombined specific nucleicacid sequences may be mixed with the original mutated specific nucleicacid sequences (parent sequences) and the cycle repeated as describedabove. In this way a set of second recombined specific nucleic acidssequences can be identified which have enhanced characteristics orencode for proteins having enhanced properties. This cycle can berepeated a number of times as desired.

It is also contemplated that in the second or subsequent recombinationcycle, a backcross can be performed. A molecular backcross can beperformed by mixing the desired specific nucleic acid sequences with alarge number of the wild-type sequence, such that at least one wild-typenucleic acid sequence and a mutated nucleic acid sequence are present inthe same host cell after transformation. Recombination with thewild-type specific nucleic acid sequence will eliminate those neutralmutations that may affect unselected characteristics such asimmunogenicity but not the selected characteristics.

In another embodiment of this invention, it is contemplated that duringthe first round a subset of the specific nucleic acid sequences can begenerated as smaller polynucleotides by slowing or halting their PCRamplification prior to introduction into the host cell. The size of thepolynucleotides must be large enough to contain some regions of identitywith the other sequences so as to homologously recombine with the othersequences. The size of the polynucleotides will range from 0.03 kb to100 kb more preferably from 0.2 kb to 10 kb. It is also contemplatedthat in subsequent rounds, all of the specific nucleic acid sequencesother than the sequences selected from the previous round may beutilized to generate PCR polynucleotides prior to introduction into thehost cells.

The shorter polynucleotide sequences can be single-stranded ordouble-stranded. If the sequences were originally single-stranded andhave become double-stranded they can be denatured with heat, chemicalsor enzymes prior to insertion into the host cell. The reactionconditions suitable for separating the strands of nucleic acid are wellknown in the art.

The steps of this process can be repeated indefinitely, being limitedonly by the number of possible hybrids which can be achieved. After acertain number of cycles, all possible hybrids will have been achievedand further cycles are redundant.

In an embodiment the same mutated template nucleic acid is repeatedlyrecombined and the resulting recombinants selected for the desiredcharacteristic.

Therefore, the initial pool or population of mutated template nucleicacid is cloned into a vector capable of replicating in a bacteria suchas E. coli. The particular vector is not essential, so long as it iscapable of autonomous replication in E. coli. In a preferred embodiment,the vector is designed to allow the expression and production of anyprotein encoded by the mutated specific nucleic acid linked to thevector. It is also preferred that the vector contain a gene encoding fora selectable marker.

The population of vectors containing the pool of mutated nucleic acidsequences is introduced into the E. coli host cells. The vector nucleicacid sequences may be introduced by transformation, transfection orinfection in the case of phage. The concentration of vectors used totransform the bacteria is such that a number of vectors is introducedinto each cell. Once present in the cell, the efficiency of homologousrecombination is such that homologous recombination occurs between thevarious vectors. This results in the generation of hybrids (daughters)having a combination of mutations which differ from the original parentmutated sequences.

The host cells are then clonally replicated and selected for the markergene present on the vector. Only those cells having a plasmid will growunder the selection.

The host cells which contain a vector are then tested for the presenceof favorable mutations. Such testing may consist of placing the cellsunder selective pressure, for example, if the gene to be selected is animproved drug resistance gene. If the vector allows expression of theprotein encoded by the mutated nucleic acid sequence, then suchselection may include allowing expression of the protein so encoded,isolation of the protein and testing of the protein to determinewhether, for example, it binds with increased efficiency to the ligandof interest.

Once a particular daughter mutated nucleic acid sequence has beenidentified which confers the desired characteristics, the nucleic acidis isolated either already linked to the vector or separated from thevector. This nucleic acid is then mixed with the first or parentpopulation of nucleic acids and the cycle is repeated.

It has been shown that by this method nucleic acid sequences havingenhanced desired properties can be selected.

In an alternate embodiment, the first generation of hybrids are retainedin the cells and the parental mutated sequences are added again to thecells. Accordingly, the first cycle of Embodiment I is conducted asdescribed above. However, after the daughter nucleic acid sequences areidentified, the host cells containing these sequences are retained.

The parent mutated specific nucleic acid population, either aspolynucleotides or cloned into the same vector is introduced into thehost cells already containing the daughter nucleic acids. Recombinationis allowed to occur in the cells and the next generation ofrecombinants, or granddaughters are selected by the methods describedabove.

This cycle can be repeated a number of times until the nucleic acid orpeptide having the desired characteristics is obtained. It iscontemplated that in subsequent cycles, the population of mutatedsequences which are added to the preferred hybrids may come from theparental hybrids or any subsequent generation.

In an alternative embodiment, the invention provides a method ofconducting a “molecular” backcross of the obtained recombinant specificnucleic acid in order to eliminate any neutral mutations. Neutralmutations are those mutations which do not confer onto the nucleic acidor peptide the desired properties. Such mutations may however confer onthe nucleic acid or peptide undesirable characteristics. Accordingly, itis desirable to eliminate such neutral mutations. The method of thisinvention provide a means of doing so.

In this embodiment, after the hybrid nucleic acid, having the desiredcharacteristics, is obtained by the methods of the embodiments, thenucleic acid, the vector having the nucleic acid or the host cellcontaining the vector and nucleic acid is isolated.

The nucleic acid or vector is then introduced into the host cell with alarge excess of the wild-type nucleic acid. The nucleic acid of thehybrid and the nucleic acid of the wild-type sequence are allowed torecombine. The resulting recombinants are placed under the sameselection as the hybrid nucleic acid. Only those recombinants whichretained the desired characteristics will be selected. Any silentmutations which do not provide the desired characteristics will be lostthrough recombination with the wild-type DNA. This cycle can be repeateda number of times until all of the silent mutations are eliminated.

Thus the methods of this invention can be used in a molecular backcrossto eliminate unnecessary or silent mutations.

2.11.2.2. Exonuclease-Mediated Reassembly

In a particular embodiment, this invention provides for a method forshuffling, assembling, reassembling, recombining, &/or concatenating atleast two polynucleotides to form a progeny polynucleotide (e.g. achimeric progeny polynucleotide that can be expressed to produce apolypeptide or a gene pathway). In a particular embodiment, a doublestranded polynucleotide end (e.g. two single stranded sequenceshybridized to each other as hybridization partners) is treated with anexonuclease to liberate nucleotides from one of the two strands, leavingthe remaining strand free of its original partner so that, if desired,the remaining strand may be used to achieve hybridization to anotherpartner.

In a particular aspect, a double stranded polynucleotide end (that maybe part of—or connected to—a polynucleotide or a nonpolynucleotidesequence) is subjected to a source of exonuclease activity. Serviceablesources of exonuclease activity may be an enzyme with 3′ exonucleaseactivity, an enzyme with 5′ exonuclease activity, an enzyme with both 3′exonuclease activity and 5′ exonuclease activity, and any combinationthereof. An exonuclease can be used to liberate nucleotides from one orboth ends of a linear double stranded polynucleotide, and from one toall ends of a branched polynucleotide having more than two ends. Themechanism of action of this liberation is believed to be comprised of anenzymatically-catalyzed hydrolysis of terminal nucleotides, and can beallowed to proceed in a time-dependent fashion, allowing experimentalcontrol of the progression of the enzymatic process.

By contrast, a non-enzymatic step may be used to shuffle, assemble,reassemble, recombine, and/or concatenate polynucleotide building blocksthat is comprised of subjecting a working sample to denaturing (or“melting”) conditions (for example, by changing temperature, pH, and/orsalinity conditions) so as to melt a working set of double strandedpolynucleotides into single polynucleotide strands. For shuffling, it isdesirable that the single polynucleotide strands participate to someextent in annealment with different hybridization partners (i.e. and notmerely revert to exclusive reannealment between what were formerpartners before the denaturation step). The presence of the formerhybridization partners in the reaction vessel, however, does notpreclude, and may sometimes even favor, reannealment of a singlestranded polynucleotide with its former partner, to recreate an originaldouble stranded polynucleotide.

In contrast to this non-enzymatic shuffling step comprised of subjectingdouble stranded polynucleotide building blocks to denaturation, followedby annealment, the instant invention further provides anexonuclease-based approach requiring no denaturation—rather, theavoidance of denaturing conditions and the maintenance of doublestranded polynucleotide substrates in annealed (i.e. non-denatured)state are necessary conditions for the action of exonucleases (e.g.,exonuclease III and red alpha gene product). Additionally in contrast,the generation of single stranded polynucleotide sequences capable ofhybridizing to other single stranded polynucleotide sequences is theresult of covalent cleavage—and hence sequence destruction—in one of thehybridization partners. For example, an exonuclease III enzyme may beused to enzymatically liberate 3′ terminal nucleotides in onehybridization strand (to achieve covalent hydrolysis in thatpolynucleotide strand); and this favors hybridization of the remainingsingle strand to a new partner (since its former partner was subjectedto covalent cleavage).

By way of further illustration, a specific exonuclease, namelyexonuclease III is provided herein as an example of a 3′ exonuclease;however, other exonucleases may also be used, including enzymes with 5′exonuclease activity and enzymes with 3′ exonuclease activity, andincluding enzymes not yet discovered and enzymes not yet developed. Itis particularly appreciated that enzymes can be discovered, optimized(e.g. engineered by directed evolution), or both discovered andoptimized specifically for the instantly disclosed approach that havemore optimal rates &/or more highly specific activities &/or greaterlack of unwanted activities. In fact it is expected that the instantinvention may encourage the discovery &/or development of such designerenzymes. In sum, this invention may be practiced with a variety ofcurrently available exonuclease enzymes, as well as enzymes not yetdiscovered and enzymes not yet developed.

The exonuclease action of exonuclease III requires a working doublestranded polynucleotide end that is either blunt or has a 5′ overhang,and the exonuclease action is comprised of enzymatically liberating 3′terminal nucleotides, leaving a single stranded 5′ end that becomeslonger and longer as the exonuclease action proceeds (see FIG. 1). Any5′ overhangs produced by this approach may be used to hybridize toanother single stranded polynucleotide sequence (which may also be asingle stranded polynucleotide or a terminal overhang of a partiallydouble stranded polynucleotide) that shares enough homology to allowhybridization. The ability of these exonuclease III-generated singlestranded sequences (e.g. in 5′ overhangs) to hybridize to other singlestranded sequences allows two or more polynucleotides to be shuffled,assembled, reassembled, &/or concatenated.

Furthermore, it is appreciated that one can protect the end of a doublestranded polynucleotide or render it susceptible to a desired enzymaticaction of a serviceable exonuclease as necessary. For example, a doublestranded polynucleotide end having a 3′ overhang is not susceptible tothe exonuclease action of exonuclease III. However, it may be renderedsusceptible to the exonuclease action of exonuclease III by a variety ofmeans; for example, it may be blunted by treatment with a polymerase,cleaved to provide a blunt end or a 5′ overhang, joined (ligated orhybridized) to another double stranded polynucleotide to provide a bluntend or a 5′ overhang, hybridized to a single stranded polynucleotide toprovide a blunt end or a 5′ overhang, or modified by any of a variety ofmeans).

According to one aspect, an exonuclease may be allowed to act on one oron both ends of a linear double stranded polynucleotide and proceed tocompletion, to near completion, or to partial completion. When theexonuclease action is allowed to go to completion, the result will bethat the length of each 5′ overhang will extend far towards the middleregion of the polynucleotide in the direction of what might beconsidered a “rendezvous point” (which may be somewhere near thepolynucleotide midpoint). Ultimately, this results in the production ofsingle stranded polynucleotides (that can become dissociated) that areeach about half the length of the original double strandedpolynucleotide (see FIG. 1). Alternatively, an exonuclease-mediatedreaction can be terminated before proceeding to completion.

Thus this exonuclease-mediated approach is serviceable for shuffling,assembling &/or reassembling, recombining, and concatenatingpolynucleotide building blocks, which polynucleotide building blocks canbe up to ten bases long or tens of bases long or hundreds of bases longor thousands of bases long or tens of thousands of bases long orhundreds of thousands of bases long or millions of bases long or evenlonger.

This exonuclease-mediated approach is based on the action of doublestranded DNA specific exodeoxyribonuclease activity of E. coliexonuclease III. Substrates for exonuclease III may be generated bysubjecting a double stranded polynucleotide to fragmentation.Fragmentation may be achieved by mechanical means (e.g., shearing,sonication, etc.), by enzymatic means (e.g. using restriction enzymes),and by any combination thereof. Fragments of a larger polynucleotide mayalso be generated by polymerase-mediated synthesis.

Exonuclease m is a 28K monomeric enzyme, product of the xthA gene of E.coli with four known activities: exodeoxyribonuclease (alternativelyreferred to as exonuclease herein), RNaseH, DNA-3′-phosphatase, and APendonuclease. The exodeoxyribonuclease activity is specific for doublestranded DNA. The mechanism of action is thought to involve enzymatichydrolysis of DNA from a 3′ end progressively towards a 5′ direction,with formation of nucleoside 5′-phosphates and a residual single strand.The enzyme does not display efficient hydrolysis of single stranded DNA,single-stranded RNA, or double-stranded RNA; however it degrades RNA inan DNA-RNA hybrid releasing nucleoside 5′-phosphates. The enzyme alsoreleases inorganic phosphate specifically from 3′phosphomonoester groupson DNA, but not from RNA or short oligonucleotides. Removal of thesegroups converts the terminus into a primer for DNA polymerase action.

Additional examples of enzymes with exonuclease activity includered-alpha and venom phosphodiesterases. Red alpha (reda) gene product(also referred to as lambda exonuclease) is of bacteriophage λ origin.The reda gene is transcribed from the leftward promoter and its productis involved (24 kD) in recombination. Red alpha gene product actsprocessively from 5′-phosphorylated termini to liberate mononucleotidesfrom duplex DNA (Takahashi & Kobayashi, 1990). Venom phosphodiesterases(Laskowski, 1980) is capable of rapidly opening supercoiled DNA.

2.11.2.3. Non-Stochastic Ligation Reassembly

In one aspect, the present invention provides a non-stochastic methodtermed synthetic ligation reassembly (SLR), that is somewhat related tostochastic shuffling, save that the nucleic acid building blocks are notshuffled or concatenated or chimerized randomly, but rather areassembled non-stochastically.

A particularly glaring difference is that the instant SLR method doesnot depend on the presence of a high level of homology betweenpolynucleotides to be shuffled. In contrast, prior methods, particularlyprior stochastic shuffling methods require that presence of a high levelof homology, particularly at coupling sites, between polynucleotides tobe shuffled. Accordingly these prior methods favor the regeneration ofthe original progenitor molecules, and are suboptimal for generatinglarge numbers of novel progeny chimeras, particularly full-lengthprogenies. The instant invention, on the other hand, can be used tonon-stochastically generate libraries (or sets) of progeny moleculescomprised of over 10¹⁰⁰ different chimeras. Conceivably, SLR can even beused to generate libraries comprised of over 10¹⁰⁰⁰ different progenychimeras with (no upper limit in sight).

Thus, in one aspect, the present invention provides a method, whichmethod is non-stochastic, of producing a set of finalized chimericnucleic acid molecules having an overall assembly order that is chosenby design, which method is comprised of the steps of generating bydesign a plurality of specific nucleic acid building blocks havingserviceable mutually compatible ligatable ends, and assembling thesenucleic acid building blocks, such that a designed overall assemblyorder is achieved.

The mutually compatible ligatable ends of the nucleic acid buildingblocks to be assembled are considered to be “serviceable” for this typeof ordered assembly if they enable the building blocks to be coupled inpredetermined orders. Thus, in one aspect, the overall assembly order inwhich the nucleic acid building blocks can be coupled is specified bythe design of the ligatable ends and, if more than one assembly step isto be used, then the overall assembly order in which the nucleic acidbuilding blocks can be coupled is also specified by the sequential orderof the assembly step(s). FIG. 4, Panel C illustrates an exemplaryassembly process comprised of 2 sequential steps to achieve a designed(non-stochastic) overall assembly order for five nucleic acid buildingblocks. In a preferred embodiment of this invention, the annealedbuilding pieces are treated with an enzyme, such as a ligase (e.g. T4DNA ligase), achieve covalent bonding of the building pieces.

In a preferred embodiment, the design of nucleic acid building blocks isobtained upon analysis of the sequences of a set of progenitor nucleicacid templates that serve as a basis for producing a progeny set offinalized chimeric nucleic acid molecules. These progenitor nucleic acidtemplates thus serve as a source of sequence information that aids inthe design of the nucleic acid building blocks that are to bemutagenized, i.e. chimerized or shuffled.

In one exemplification, this invention provides for the chimerization ofa family of related genes and their encoded family of related products.In a particular exemplification, the encoded products are enzymes. As arepresentative list of families of enzymes which may be mutagenized inaccordance with the aspects of the present invention, there may bementioned, the following enzymes and their functions:

1 Lipase/Esterase

-   -   a. Enantioselective hydrolysis of esters (lipids)/thioesters        -   1) Resolution of racemic mixtures        -   2) Synthesis of optically active acids or alcohols from            meso-diesters    -   b. Selective syntheses        -   1) Regiospecific hydrolysis of carbohydrate esters        -   2) Selective hydrolysis of cyclic secondary alcohols    -   c. Synthesis of optically active esters, lactones, acids,        alcohols        -   1) Transesterification of activated/nonactivated esters        -   2) Interesterification        -   3) Optically active lactones from hydroxyesters        -   4) Regio- and enantioselective ring opening of anhydrides    -   d. Detergents    -   e. Fat/Oil conversion    -   f. Cheese ripening

2 Protease

-   -   a. Ester/amide synthesis    -   b. Peptide synthesis    -   c. Resolution of racemic mixtures of amino acid esters    -   d. Synthesis of non-natural amino acids    -   e. Detergents/protein hydrolysis        3 Glycosidase/Glycosyl transferase    -   a. Sugar/polymer synthesis    -   b. Cleavage of glycosidic linkages to form mono, di- and        oligosaccharides    -   c. Synthesis of complex oligosaccharides    -   d. Glycoside synthesis using UDP-galactosyl transferase    -   e. Transglycosylation of disaccharides, glycosyl fluorides, aryl        galactosides    -   f. Glycosyl transfer in oligosaccharide synthesis    -   g. Diastereoselective cleavage of β-glucosylsulfoxides    -   h. Asymmetric glycosylations    -   i. Food processing    -   j. Paper processing

4 Phosphatase/Kinase

-   -   a. Synthesis/hydrolysis of phosphate esters        -   1) Regio-, enantioselective phosphorylation        -   2) Introduction of phosphate esters        -   3) Synthesize phospholipid precursors        -   4) Controlled polynucleotide synthesis    -   b. Activate biological molecule    -   c. Selective phosphate bond formation without protecting groups

5 Mono/Dioxygenase

-   -   a. Direct oxyfunctionalization of unactivated organic substrates    -   b. Hydroxylation of alkane, aromatics, steroids    -   c. Epoxidation of alkenes    -   d. Enantioselective sulphoxidation    -   e. Regio- and stereoselective Bayer-Villiger oxidations

6 Haloperoxidase

-   -   a. Oxidative addition of halide ion to nucleophilic sites    -   b. Addition of hypohalous acids to olefinic bonds    -   c. Ring cleavage of cyclopropanes    -   d. Activated aromatic substrates converted to ortho and para        derivatives    -   e. 1.3 diketones converted to 2-halo-derivatives    -   f. Heteroatom oxidation of sulfur and nitrogen containing        substrates    -   g. Oxidation of enol acetates, alkynes and activated aromatic        rings        7 Lignin peroxidase/Diarylpropane peroxidase    -   a. Oxidative cleavage of C—C bonds    -   b. Oxidation of benzylic alcohols to aldehydes    -   c. Hydroxylation of benzylic carbons    -   d. Phenol dimerization    -   e. Hydroxylation of double bonds to form diols    -   f. Cleavage of lignin aldehydes        8 Epoxide hydrolase    -   a. Synthesis of enantiomerically pure bioactive compounds    -   b. Regio- and enantioselective hydrolysis of epoxide    -   c. Aromatic and olefinic epoxidation by monooxygenases to form        epoxides    -   d. Resolution of racemic epoxides    -   e. Hydrolysis of steroid epoxides        9 Nitrile hydratase/nitrilase    -   a. Hydrolysis of aliphatic nitrites to carboxamides    -   b. Hydrolysis of aromatic, heterocyclic, unsaturated aliphatic        nitrites to corresponding acids    -   c. Hydrolysis of acrylonitrile    -   d. Production of aromatic and carboxamides, carboxylic acids        (nicotinamide, picolinamide, isonicotinamide)    -   e. Regioselective hydrolysis of acrylic dinitrile    -   f. α-amino acids from α-hydroxynitriles

10 Transaminase

-   -   a. Transfer of amino groups into oxo-acids

11 Amidase/Acylase

-   -   a. Hydrolysis of amides, amidines, and other C—N bonds    -   b. Non-natural amino acid resolution and synthesis

These exemplifications, while illustrating certain specific aspects ofthe invention, do not portray the limitations or circumscribe the scopeof the disclosed invention.

Thus according to one aspect of this invention, the sequences of aplurality of progenitor nucleic acid templates are aligned in order toselect one or more demarcation points, which demarcation points can belocated at an area of homology, and are comprised of one or morenucleotides, and which demarcation points are shared by at least two ofthe progenitor templates. The demarcation points can be used todelineate the boundaries of nucleic acid building blocks to begenerated. Thus, the demarcation points identified and selected in theprogenitor molecules serve as potential chimerization points in theassembly of the progeny molecules.

Preferably a serviceable demarcation point is an area of homology(comprised of at least one homologous nucleotide base) shared by atleast two progenitor templates. More preferably a serviceabledemarcation point is an area of homology that is shared by at least halfof the progenitor templates. More preferably still a serviceabledemarcation point is an area of homology that is shared by at least twothirds of the progenitor templates. Even more preferably a serviceabledemarcation points is an area of homology that is shared by at leastthree fourths of the progenitor templates. Even more preferably still aserviceable demarcation points is an area of homology that is shared byat almost all of the progenitor templates. Even more preferably still aserviceable demarcation point is an area of homology that is shared byall of the progenitor templates.

The process of designing nucleic acid building blocks and of designingthe mutually compatible ligatable ends of the nucleic acid buildingblocks to be assembled is illustrated in FIGS. 6 and 7. As shown, thealignment of a set of progenitor templates reveals several naturallyoccurring demarcation points, and the identification of demarcationpoints shared by these templates helps to non-stochastically determinethe building blocks to be generated and used for the generation of theprogeny chimeric molecules.

In a preferred embodiment, this invention provides that the ligationreassembly process is performed exhaustively in order to generate anexhaustive library. In other words, all possible ordered combinations ofthe nucleic acid building blocks are represented in the set of finalizedchimeric nucleic acid molecules. At the same time, in a particularlypreferred embodiment, the assembly order (i.e. the order of assembly ofeach building block in the 5′ to 3′ sequence of each finalized chimericnucleic acid) in each combination is by design (or non-stochastic).Because of the non-stochastic nature of this invention, the possibilityof unwanted side products is greatly reduced.

In another preferred embodiment, this invention provides that theligation reassembly process is performed systematically, for example inorder to generate a systematically compartmentalized library, withcompartments that can be screened systematically, e.g. one by one. Inother words this invention provides that, through the selective andjudicious use of specific nucleic acid building blocks, coupled with theselective and judicious use of sequentially stepped assembly reactions,an experimental design can be achieved where specific sets of progenyproducts are made in each of several reaction vessels. This allows asystematic examination and screening procedure to be performed. Thus, itallows a potentially very large number of progeny molecules to beexamined systematically in smaller groups.

Because of its ability to perform chimerizations in a manner that ishighly flexible yet exhaustive and systematic as well, particularly whenthere is a low level of homology among the progenitor molecules, theinstant invention provides for the generation of a library (or set)comprised of a large number of progeny molecules. Because of thenon-stochastic nature of the instant ligation reassembly invention, theprogeny molecules generated preferably comprise a library of finalizedchimeric nucleic acid molecules having an overall assembly order that ischosen by design. In a particularly preferred embodiment of thisinvention, such a generated library is comprised of preferably greaterthan 10³ different progeny molecular species, more preferably greaterthan 10⁵ different progeny molecular species, more preferably stillgreater than 10¹⁰ different progeny molecular species, more preferablystill greater than 10¹⁵ different progeny molecular species, morepreferably still greater than 10²⁰ different progeny molecular species,more preferably still greater than 10³⁰ different progeny molecularspecies, more preferably still greater than 10⁴⁰ different progenymolecular species, more preferably still greater than 10⁵⁰ differentprogeny molecular species, more preferably still greater than 10⁶⁰different progeny molecular species, more preferably still greater than10⁷⁰ different progeny molecular species, more preferably still greaterthan 10⁸⁰ different progeny molecular species, more preferably stillgreater than 10¹⁰⁰ different progeny molecular species, more preferablystill greater than 10¹¹⁰ different progeny molecular species, morepreferably still greater than 10¹²⁰ different progeny molecular species,more preferably still greater than 10¹³⁰ different progeny molecularspecies, more preferably still greater than 10¹⁴⁰ different progenymolecular species, more preferably still greater than 10¹⁵⁰ differentprogeny molecular species, more preferably still greater than 10¹⁷⁵different progeny molecular species, more preferably still greater than10²⁰⁰ different progeny molecular species, more preferably still greaterthan 10³⁰⁰ different progeny molecular species, more preferably stillgreater than 10⁴⁰⁰ different progeny molecular species, more preferablystill greater than 10⁵⁰⁰ different progeny molecular species, and evenmore preferably still greater than 10¹⁰⁰⁰ different progeny molecularspecies.

In one aspect, a set of finalized chimeric nucleic acid molecules,produced as described is comprised of a polynucleotide encoding apolypeptide. According to one preferred embodiment, this polynucleotideis a gene, which may be a man-made gene. According to another preferredembodiment, this polynucleotide is a gene pathway, which may be aman-made gene pathway. This invention provides that one or more man-madegenes generated by this invention may be incorporated into a man-madegene pathway, such as a pathway operable in a eukaryotic organism(including a plant).

It is appreciated that the power of this invention is exceptional, asthere is much freedom of choice and control regarding the selection ofdemarcation points, the size and number of the nucleic acid buildingblocks, and the size and design of the couplings. It is appreciated,furthermore, that the requirement for intermolecular homology is highlyrelaxed for the operability of this invention. In fact, demarcationpoints can even be chosen in areas of little or no intermolecularhomology. For example, because of codon wobble, i.e. the degeneracy ofcodons, nucleotide substitutions can be introduced into nucleic acidbuilding blocks without altering the amino acid originally encoded inthe corresponding progenitor template. Alternatively, a codon can bealtered such that the coding for an original amino acid is altered. Thisinvention provides that such substitutions can be introduced into thenucleic acid building block in order to increase the incidence ofintermolecularly homologous demarcation points and thus to allow anincreased number of couplings to be achieved among the building blocks,which in turn allows a greater number of progeny chimeric molecules tobe generated.

In another exemplification, the synthetic nature of the step in whichthe building blocks are generated allows the design and introduction ofnucleotides (e.g. one or more nucleotides, which may be, for example,codons or introns or regulatory sequences) that can later be optionallyremoved in an in vitro process (e.g. by mutagenesis) or in an in vivoprocess (e.g. by utilizing the gene splicing ability of a hostorganism). It is appreciated that in many instances the introduction ofthese nucleotides may also be desirable for many other reasons inaddition to the potential benefit of creating a serviceable demarcationpoint.

Thus, according to another embodiment, this invention provides that anucleic acid building block can be used to introduce an intron. Thus,this invention provides that functional introns may be introduced into aman-made gene of this invention. This invention also provides thatfunctional introns may be introduced into a man-made gene pathway ofthis invention. Accordingly, this invention provides for the generationof a chimeric polynucleotide that is a man-made gene containing one (ormore) artificially introduced intron(s).

Accordingly, this invention also provides for the generation of achimeric polynucleotide that is a man-made gene pathway containing one(or more) artificially introduced intron(s). Preferably, theartificially introduced intron(s) are functional in one or more hostcells for gene splicing much in the way that naturally-occurring intronsserve functionally in gene splicing. This invention provides a processof producing man-made intron-containing polynucleotides to be introducedinto host organisms for recombination and/or splicing.

The ability to achieve chimerizations, using couplings as describedherein, in areas of little or no homology among the progenitormolecules, is particularly useful, and in fact critical, for theassembly of novel gene pathways. This invention thus provides for thegeneration of novel man-made gene pathways using synthetic ligationreassembly. In a particular aspect, this is achieved by the introductionof regulatory sequences, such as promoters, that are operable in anintended host, to confer operability to a novel gene pathway when it isintroduced into the intended host. In a particular exemplification, thisinvention provides for the generation of novel man-made gene pathwaysthat is operable in a plurality of intended hosts (e.g. in a microbialorganism as well as in a plant cell). This can be achieved, for example,by the introduction of a plurality of regulatory sequences, comprised ofa regulatory sequence that is operable in a first intended host and aregulatory sequence that is operable in a second intended host. Asimilar process can be performed to achieve operability of a genepathway in a third intended host species, etc. The number of intendedhost species can be each integer from 1 to 10 or alternatively over 10.Alternatively, for example, operability of a gene pathway in a pluralityof intended hosts can be achieved by the introduction of a regulatorysequence having intrinsic operability in a plurality of intended hosts.

Thus, according to a particular embodiment, this invention provides thata nucleic acid building block can be used to introduce a regulatorysequence, particularly a regulatory sequence for gene expression.Preferred regulatory sequences include, but are not limited to, thosethat are man-made, and those found in archeal, bacterial, eukaryotic(including mitochondrial), viral, and prionic or prion-like organisms.Preferred regulatory sequences include but are not limited to,promoters, operators, and activator binding sites. Thus, this inventionprovides that functional regulatory sequences may be introduced into aman-made gene of this invention. This invention also provides thatfunctional regulatory sequences may be introduced into a man-made genepathway of this invention.

Accordingly, this invention provides for the generation of a chimericpolynucleotide that is a man-made gene containing one (or more)artificially introduced regulatory sequence(s). Accordingly, thisinvention also provides for the generation of a chimeric polynucleotidethat is a man-made gene pathway containing one (or more) artificiallyintroduced regulatory sequence(s). Preferably, an artificiallyintroduced regulatory sequence(s) is operatively linked to one or moregenes in the man-made polynucleotide, and are functional in one or morehost cells.

Preferred bacterial promoters that are serviceable for this inventioninclude lac, lacZ, T3, T7, gpt, lambda P_(R), P_(L) and trp. Serviceableeukaryotic promoters include CMV immediate early, HSV thymidine kinase,early and late SV40, LTRs from retrovirus, and mouse metallothionein-I.Particular plant regulatory sequences include promoters active indirecting transcription in plants, either constitutively or stage and/ortissue specific, depending on the use of the plant or parts thereof.These promoters include, but are not limited to promoters showingconstitutive expression, such as the 35S promoter of Cauliflower MosaicVirus (CaMV) (Guilley et al., 1982), those for leaf-specific expression,such as the promoter of the ribulose bisphosphate carboxylase smallsubunit gene (Coruzzi et al., 1984), those for root-specific expression,such as the promoter from the glutamin synthase gene (Tingey et al.,1987), those for seed-specific expression, such as the cruciferin Apromoter from Brassica napus (Ryan et al., 1989), those fortuber-specific expression, such as the class-I patatin promoter frompotato (Rocha-Sasa et al., 1989; Wenzler et al., 1989) or those forfruit-specific expression, such as the polygalacturonase (PG) promoterfrom tomato (Bird et al., 1988).

Other regulatory sequences that are preferred for this invention includeterminator sequences and polyadenylation signals and any such sequencefunctioning as such in plants, the choice of which is within the levelof the skilled artisan. An example of such sequences is the 3′ flankingregion of the nopaline synthase (nos) gene of Agrobacterium tumefaciens(Bevan, 1984). The regulatory sequences may also include enhancersequences, such as found in the 35S promoter of CaMV, and mRNAstabilizing sequences such as the leader sequence of Alfalfa MosaicCirus (AlMV) RNA4 (Brederode et al., 1980) or any other sequencesfunctioning in a like manner.

Man-made genes produced using this invention can also serve as asubstrate for recombination with another nucleic acid. Likewise, aman-made gene pathway produced using this invention can also serve as asubstrate for recombination with another nucleic acid. In a preferredinstance, the recombination is facilitated by, or occurs at, areas ofhomology between the man-made intron-containing gene and a nucleic acidwith serves as a recombination partner. In a particularly preferredinstance, the recombination partner may also be a nucleic acid generatedby this invention, including a man-made gene or a man-made gene pathway.Recombination may be facilitated by or may occur at areas of homologythat exist at the one (or more) artificially introduced intron(s) in theman-made gene.

The synthetic ligation reassembly method of this invention utilizes aplurality of nucleic acid building blocks, each of which preferably hastwo ligatable ends. The two ligatable ends on each nucleic acid buildingblock may be two blunt ends (i.e. each having an overhang of zeronucleotides), or preferably one blunt end and one overhang, or morepreferably still two overhangs.

A serviceable overhang for this purpose may be a 3′ overhang or a 5′overhang. Thus, a nucleic acid building block may have a 3′ overhang oralternatively a 5′ overhang or alternatively two 3′ overhangs oralternatively two 5′ overhangs. The overall order in which the nucleicacid building blocks are assembled to form a finalized chimeric nucleicacid molecule is determined by purposeful experimental design and is notrandom.

According to one preferred embodiment, a nucleic acid building block isgenerated by chemical synthesis of two single-stranded nucleic acids(also referred to as single-stranded oligos) and contacting them so asto allow them to anneal to form a double-stranded nucleic acid buildingblock.

A double-stranded nucleic acid building block can be of variable size.The sizes of these building blocks can be small or large depending onthe choice of the experimenter. Preferred sizes for building block rangefrom 1 base pair (not including any overhangs) to 100,000 base pairs(not including any overhangs). Other preferred size ranges are alsoprovided, which have lower limits of from 1 bp to 10,000 bp (includingevery integer value in between), and upper limits of from 2 bp to100,000 bp (including every integer value in between).

It is appreciated that current methods of polymerase-based amplificationcan be used to generate double-stranded nucleic acids of up to thousandsof base pairs, if not tens of thousands of base pairs, in length withhigh fidelity. Chemical synthesis (e.g. phosphoramidite-based) can beused to generate nucleic acids of up to hundreds of nucleotides inlength with high fidelity; however, these can be assembled, e.g. usingoverhangs or sticky ends, to form double-stranded nucleic acids of up tothousands of base pairs, if not tens of thousands of base pairs, inlength if so desired.

A combination of methods (e.g. phosphoramidite-based chemical synthesisand PCR) can also be used according to this invention. Thus, nucleicacid building block made by different methods can also be used incombination to generate a progeny molecule of this invention.

The use of chemical synthesis to generate nucleic acid building blocksis particularly preferred in this invention & is advantageous for otherreasons as well, including procedural safety and ease. No cloning orharvesting or actual handling of any biological samples is required. Thedesign of the nucleic acid building blocks can be accomplished on paper.Accordingly, this invention teaches an advance in procedural safety inrecombinant technologies.

Nonetheless, according to one preferred embodiment, a double-strandednucleic acid building block according to this invention may also begenerated by polymerase-based amplification of a polynucleotidetemplate. In a non-limiting exemplification, as illustrated in FIG. 2, afirst polymerase-based amplification reaction using a first set ofprimers, F₂ and R₁, is used to generate a blunt-ended product (labeledReaction 1, Product 1), which is essentially identical to Product A. Asecond polymerase-based amplification reaction using a second set ofprimers, F₁ and R₂, is used to generate a blunt-ended product (labeledReaction 2, Product 2), which is essentially identical to Product B.These two products are mixed and allowed to melt and anneal, generatingpotentially useful double-stranded nucleic acid building blocks with twooverhangs. In the example of FIG. 2, the product with the 3′ overhangs(Product C) is selected by nuclease-based degradation of the other 3products using a 3′ acting exonuclease, such as exonuclease III. It isappreciated that a 5′ acting exonuclease (e.g. red alpha) may be also beused, for example to select Product D instead. It is also appreciatedthat other selection means can also be used, includinghybridization-based means, and that these means can incorporate afurther means, such as a magnetic bead-based means, to facilitateseparation of the desired product.

Many other methods exist by which a double-stranded nucleic acidbuilding block can be generated that is serviceable for this invention;and these are known in the art and can be readily performed by theskilled artisan.

According to particularly preferred embodiment, a double-strandednucleic acid building block that is serviceable for this invention isgenerated by first generating two single stranded nucleic acids andallowing them to anneal to form a double-stranded nucleic acid buildingblock. The two strands of a double-stranded nucleic acid building blockmay be complementary at every nucleotide apart from any that form anoverhang; thus containing no mismatches, apart from any overhang(s).According to another embodiment, the two strands of a double-strandednucleic acid building block are complementary at fewer than everynucleotide apart from any that form an overhang. Thus, according to thisembodiment, a double-stranded nucleic acid building block can be used tointroduce codon degeneracy. Preferably the codon degeneracy isintroduced using the site-saturation mutagenesis described herein, usingone or more N,N,G/T cassettes or alternatively using one or more N,N,Ncassettes.

Contained within an exemplary experimental design for achieving anordered assembly according to this invention are:

1) The design of specific nucleic acid building blocks.

2) The design of specific ligatable ends on each nucleic acid buildingblock.

3) The design of a particular order of assembly of the nucleic acidbuilding blocks.

An overhang may be a 3′ overhang or a 5′ overhang. An overhang may alsohave a terminal phosphate group or alternatively may be devoid of aterminal phosphate group (having, e.g., a hydroxyl group instead). Anoverhang may be comprised of any number of nucleotides. Preferably anoverhang is comprised of 0 nucleotides (as in a blunt end) to 10,000nucleotides. Thus, a wide range of overhang sizes may be serviceable.Accordingly, the lower limit may be each integer from 1-200 and theupper limit may be each integer from 2-10,000. According to a particularexemplification, an overhang may consist of anywhere from 1 nucleotideto 200 nucleotides (including every integer value in between).

The final chimeric nucleic acid molecule may be generated bysequentially assembling 2 or more building blocks at a time until allthe designated building blocks have been assembled. A working sample mayoptionally be subjected to a process for size selection or purificationor other selection or enrichment process between the performance of twoassembly steps. Alternatively, the final chimeric nucleic acid moleculemay be generated by assembling all the designated building blocks atonce in one step.

Utility

The in vivo recombination method of this invention can be performedblindly on a pool of unknown hybrids or alleles of a specificpolynucleotide or sequence. However, it is not necessary to know theactual DNA or RNA sequence of the specific polynucleotide.

The approach of using recombination within a mixed population of genescan be useful for the generation of any useful proteins, for example,interleukin I, antibodies, tPA and growth hormone. This approach may beused to generate proteins having altered specificity or activity. Theapproach may also be useful for the generation of hybrid nucleic acidsequences, for example, promoter regions, introns, exons, enhancersequences, 31 untranslated regions or 51 untranslated regions of genes.Thus this approach may be used to generate genes having increased ratesof expression. This approach may also be useful in the study ofrepetitive DNA sequences. Finally, this approach may be useful to mutateribozymes or aptamers.

Scaffold-like regions separating regions of diversity in proteins may beparticularly suitable for the methods of this invention. The conservedscaffold determines the overall folding by self-association, whiledisplaying relatively unrestricted loops that mediate the specificbinding. Examples of such scaffolds are the immunoglobulin beta barrel,and the four-helix bundle. The methods of this invention can be used tocreate scaffold-like proteins with various combinations of mutatedsequences for binding.

The equivalents of some standard genetic matings may also be performedby the methods of this invention. For example, a “molecular” backcrosscan be performed by repeated mixing of the hybrid's nucleic acid withthe wild-type nucleic acid while selecting for the mutations ofinterest. As in traditional breeding, this approach can be used tocombine phenotypes from different sources into a background of choice.It is useful, for example, for the removal of neutral mutations thataffect unselected characteristics (i.e. immunogenicity). Thus it can beuseful to determine which mutations in a protein are involved in theenhanced biological activity and which are not.

2.11.2.4. End-Selection

This invention provides a method for selecting a subset ofpolynucleotides from a starting set of polynucleotides, which method isbased on the ability to discriminate one or more selectable features (orselection markers) present anywhere in a working polynucleotide, so asto allow one to perform selection for (positive selection) &/or against(negative selection) each selectable polynucleotide. In a preferredaspect, a method is provided termed end-selection, which method is basedon the use of a selection marker located in part or entirely in aterminal region of a selectable polynucleotide, and such a selectionmarker may be termed an “end-selection marker”.

End-selection may be based on detection of naturally occurring sequencesor on detection of sequences introduced experimentally (including by anymutagenesis procedure mentioned herein and not mentioned herein) or onboth, even within the same polynucleotide. An end-selection marker canbe a structural selection marker or a functional selection marker orboth a structural and a functional selection marker. An end-selectionmarker may be comprised of a polynucleotide sequence or of a polypeptidesequence or of any chemical structure or of any biological orbiochemical tag, including markers that can be selected using methodsbased on the detection of radioactivity, of enzymatic activity, offluorescence, of any optical feature, of a magnetic property (e.g. usingmagnetic beads), of immunoreactivity, and of hybridization.

End-selection may be applied in combination with any method serviceablefor performing mutagenesis. Such mutagenesis methods include, but arenot limited to, methods described herein (supra and infra). Such methodsinclude, by way of non-limiting exemplification, any method that may bereferred herein or by others in the art by any of the following terms:“saturation mutagenesis”, “shuffling”, “recombination”, “re-assembly”,“error-prone PCR”, “assembly PCR”, “sexual PCR”, “crossover PCR”,“oligonucleotide primer-directed mutagenesis”, “recursive (&/orexponential) ensemble mutagenesis (see Arkin and Youvan, 1992)”,“cassette mutagenesis”, “in vivo mutagenesis”, and “in vitromutagenesis”. Moreover, end-selection may be performed on moleculesproduced by any mutagenesis &/or amplification method (see, e.g.,Arnold, 1993; Caldwell and Joyce, 1992; Stemmer, 1994; following whichmethod it is desirable to select for (including to screen for thepresence of) desirable progeny molecules.

In addition, end-selection may be applied to a polynucleotide apart fromany mutagenesis method. In a preferred embodiment, end-selection, asprovided herein, can be used in order to facilitate a cloning step, suchas a step of ligation to another polynucleotide (including ligation to avector). This invention thus provides for end-selection as a serviceablemeans to facilitate library construction, selection &/or enrichment fordesirable polynucleotides, and cloning in general.

In a particularly preferred embodiment, end-selection can be based on(positive) selection for a polynucleotide; alternatively end-selectioncan be based on (negative) selection against a polynucleotide; andalternatively still, end-selection can be based on both (positive)selection for, and on (negative) selection against, a polynucleotide.End-selection, along with other methods of selection &/or screening, canbe performed in an iterative fashion, with any combination of like orunlike selection &/or screening methods and serviceable mutagenesismethods, all of which can be performed in an iterative fashion and inany order, combination, and permutation.

It is also appreciated that, according to one embodiment of thisinvention, end-selection may also be used to select a polynucleotidethat is at least in part: circular (e.g. a plasmid or any other circularvector or any other polynucleotide that is partly circular), &/orbranched, &/or modified or substituted with any chemical group ormoiety. In accord with this embodiment, a polynucleotide may be acircular molecule comprised of an intermediate or central region, whichregion is flanked on a 5′ side by a 5′ flanking region (which, for thepurpose of end-selection, serves in like manner to a 5′ terminal regionof a non-circular polynucleotide) and on a 3′ side by a 3′ terminalregion (which, for the purpose of end-selection, serves in like mannerto a 3′ terminal region of a non-circular polynucleotide). As used inthis non-limiting exemplification, there may be sequence overlap betweenany two regions or even among all three regions.

In one non-limiting aspect of this invention, end-selection of a linearpolynucleotide is performed using a general approach based on thepresence of at least one end-selection marker located at or near apolynucleotide end or terminus (that can be either a 5′ end or a 3′end). In one particular non-limiting exemplification, end-selection isbased on selection for a specific sequence at or near a terminus suchas, but not limited to, a sequence recognized by an enzyme thatrecognizes a polynucleotide sequence. An enzyme that recognizes andcatalyzes a chemical modification of a polynucleotide is referred toherein as a polynucleotide-acting enzyme. In a preferred embodiment,serviceable polynucleotide-acting enzymes are exemplifiednon-exclusively by enzymes with polynucleotide-cleaving activity,enzymes with polynucleotide-methylating activity, enzymes withpolynucleotide-ligating activity, and enzymes with a plurality ofdistinguishable enzymatic activities (including non-exclusively, e.g.,both polynucleotide-cleaving activity and polynucleotide-ligatingactivity).

Relevant polynucleotide-acting enzymes thus also include anycommercially available or non-commercially available polynucleotideendonucleases and their companion methylases including those cataloguedat the website http://www.neb.com/rebase, and those mentioned in thefollowing cited reference (Roberts and Macelis, 1996). Preferredpolynucleotide endonucleases include—but are not limited to—type IIrestriction enzymes (including type IIS), and include enzymes thatcleave both strands of a double stranded polynucleotide (e.g. Not I,which cleaves both strands at 5′ . . . GC/GGCCGC . . . 3′) and enzymesthat cleave only one strand of a double stranded polynucleotide, i.e.enzymes that have polynucleotide-nicking activity, (e.g. N. BstNB I,which cleaves only one strand at 5′ . . . GAGTCNNNN/N . . . 3′).Relevant polynucleotide-acting enzymes also include type III restrictionenzymes.

It is appreciated that relevant polynucleotide-acting enzymes alsoinclude any enzymes that may be developed in the future, thoughcurrently unavailable, that are serviceable for generating a ligationcompatible end, preferably a sticky end, in a polynucleotide.

In one preferred exemplification, a serviceable selection marker is arestriction site in a polynucleotide that allows a corresponding type II(or type IIS) restriction enzyme to cleave an end of the polynucleotideso as to provide a ligatable end (including a blunt end or alternativelya sticky end with at least a one base overhang) that is serviceable fora desirable ligation reaction without cleaving the polynucleotideinternally in a manner that destroys a desired internal sequence in thepolynucleotide. Thus it is provided that, among relevant restrictionsites, those sites that do not occur internally (i.e. that do not occurapart from the termini) in a specific working polynucleotide arepreferred when the use of a corresponding restriction enzyme(s) is notintended to cut the working polynucleotide internally. This allows oneto perform restriction digestion reactions to completion or to nearcompletion without incurring unwanted internal cleavage in a workingpolynucleotide.

According to a preferred aspect, it is thus preferable to userestriction sites that are not contained, or alternatively that are notexpected to be contained, or alternatively that are unlikely to becontained (e.g. when sequence information regarding a workingpolynucleotide is incomplete) internally in a polynucleotide to besubjected to end-selection. In accordance with this aspect, it isappreciated that restriction sites that occur relatively infrequentlyare usually preferred over those that occur more frequently. On theother hand it is also appreciated that there are occasions whereinternal cleavage of a polypeptide is desired, e.g. to achieverecombination or other mutagenic procedures along with end-selection.

In accord with this invention, it is also appreciated that methods (e.g.mutagenesis methods) can be used to remove unwanted internal restrictionsites. It is also appreciated that a partial digestion reaction (i.e. adigestion reaction that proceeds to partial completion) can be used toachieve digestion at a recognition site in a terminal region whilesparing a susceptible restriction site that occurs internally in apolynucleotide and that is recognized by the same enzyme. In one aspect,partial digest are useful because it is appreciated that certain enzymesshow preferential cleavage of the same recognition sequence depending onthe location and environment in which the recognition sequence occurs.For example, it is appreciated that, while lambda DNA has 5 EcoR Isites, cleavage of the site nearest to the right terminus has beenreported to occur 10 times faster than the sites in the middle of themolecule. Also, for example, it has been reported that, while Sac II hasfour sites on lambda DNA, the three clustered centrally in lambda arecleaved 50 times faster than the remaining site near the terminus (atnucleotide 40,386). Summarily, site preferences have been reported forvarious enzymes by many investigators (e.g., Thomas and Davis, 1975;Forsblum et al, 1976; Nath and Azzolina, 1981; Brown and Smith, 1977;Gingeras and Brooks, 1983; Krüger et al, 1988; Conrad and Topal, 1989;Oller et al, 1991; Topal, 1991; and Pein, 1991; to name but a few). Itis appreciated that any empirical observations as well as anymechanistic understandings of site preferences by any serviceablepolynucleotide-acting enzymes, whether currently available or to beprocured in the future, may be serviceable in end-selection according tothis invention.

It is also appreciated that protection methods can be used toselectively protect specified restriction sites (e.g. internal sites)against unwanted digestion by enzymes that would otherwise cut a workingpolypeptide in response to the presence of those sites; and that suchprotection methods include modifications such as methylations and basesubstitutions (e.g. U instead of T) that inhibit an unwanted enzymeactivity. It is appreciated that there are limited numbers of availablerestriction enzymes that are rare enough (e.g. having very longrecognition sequences) to create large (e.g. megabase-long) restrictionfragments, and that protection approaches (e.g. by methylation) areserviceable for increasing the rarity of enzyme cleavage sites. The useof M.Fnu II (mCGCG) to increase the apparent rarity of Not Iapproximately twofold is but one example among many (Qiang et al, 1990;Nelson et al, 1984; Maxam and Gilbert, 1980; Raleigh and Wilson, 1986).

According to a preferred aspect of this invention, it is provided that,in general, the use of rare restriction sites is preferred. It isappreciated that, in general, the frequency of occurrence of arestriction site is determined by the number of nucleotides containedtherein, as well as by the ambiguity of the base requirements containedtherein. Thus, in a non-limiting exemplification, it is appreciatedthat, in general, a restriction site composed of, for example, 8specific nucleotides (e.g. the Not I site or GC/GGCCGC, with anestimated relative occurrence of 1 in 4⁸, i.e. 1 in 65,536, random8-mers) is relatively more infrequent than one composed of, for example,6 nucleotides (e.g. the Sma I site or CCC/GGG, having an estimatedrelative occurrence of 1 in 4⁶, i.e. 1 in 4,096, random 6-mers), whichin turn is relatively more infrequent than one composed of, for example,4 nucleotides (e.g. the Msp I site or C/COG, having an estimatedrelative occurrence of 1 in 4⁴, i.e. 1 in 256, random 4-mers). Moreover,in another non-limiting exemplification, it is appreciated that, ingeneral, a restriction site having no ambiguous (but only specific) baserequirements (e.g. the Fin I site or GTCCC, having an estimated relativeoccurrence of 1 in 4⁵, i.e. 1 in 1024, random 5-mers) is relatively moreinfrequent than one having an ambiguous W (where W=A or T) baserequirement (e.g. the Ava II site or G/GWCC, having an estimatedrelative occurrence of 1 in 4×4×2×4×4—i.e. 1 in 512—random 5-mers),which in turn is relatively more infrequent than one having an ambiguousN (where N=A or C or G or T) base requirement (e.g. the Asu I site orG/GNCC, having an estimated relative occurrence of 1 in 4×4×1×4×4, i.e.1 in 256—random 5-mers). These relative occurrences are consideredgeneral estimates for actual polynucleotides, because it is appreciatedthat specific nucleotide bases (not to mention specific nucleotidesequences) occur with dissimilar frequencies in specificpolynucleotides, in specific species of organisms, and in specificgroupings of organisms. For example, it is appreciated that the % G+Ccontents of different species of organisms are often very different andwide ranging.

The use of relatively more infrequent restriction sites as a selectionmarker include—in a non-limiting fashion—preferably those sites composedof at least a 4 nucleotide sequence, more preferably those composed atleast a 5 nucleotide sequence, more preferably still those composed atleast a 6 nucleotide sequence (e.g. the BamH I site or G/GATCC, the BglII site or A/GATCT, the Pst I site or CTGCA/Q and the Xba I site orT/CTAGA), more preferably still those composed at least a 7 nucleotidesequence, more preferably still those composed of an 8 nucleotidesequence nucleotide sequence (e.g. the Asc I site or GG/CGCGCC, the NotI site or GC/GGCCGC, the Pac I site or TFAAT/TAA, the Pme I site orGTT=/AAAC, the Srf I site or GCCC/GGGC, the Sse838 I site or CCTGCA/GG,and the Swa I site or ATTT/AAAT), more preferably still those composedof a 9 nucleotide sequence, and even more preferably still thosecomposed of at least a 10 nucleotide sequence (e.g. the BspG I site orCG/CGCTGGAC). It is further appreciated that some restriction sites(e.g. for class IIS enzymes) are comprised of a portion of relativelyhigh specificity (i.e. a portion containing a principal determinant ofthe frequency of occurrence of the restriction site) and a portion ofrelatively low specificity; and that a site of cleavage may or may notbe contained within a portion of relatively low specificity. Forexample, in the Eco57 I site or CTGAAG(16/14), there is a portion ofrelatively high specificity (i.e. the CTGAAG portion) and a portion ofrelatively low specificity (i.e. the N16 sequence) that contains a siteof cleavage.

In another preferred embodiment of this invention, a serviceableend-selection marker is a terminal sequence that is recognized by apolynucleotide-acting enzyme that recognizes a specific polynucleotidesequence. In a preferred aspect of this invention, serviceablepolynucleotide-acting enzymes also include other enzymes in addition toclassic type II restriction enzymes. According to this preferred aspectof this invention, serviceable polynucleotide-acting enzymes alsoinclude gyrases, helicases, recombinases, relaxases, and any enzymesrelated thereto.

Among preferred examples are topoisomerases (which have been categorizedby some as a subset of the gyrases) and any other enzymes that havepolynucleotide-cleaving activity (including preferablypolynucleotide-nicking activity) &/or polynucleotide-ligating activity.Among preferred topoisomerase enzymes are topoisomerase I enzymes, whichis available from many commercial sources (Epicentre Technologies,Madison, Wis.; Invitrogen, Carlsbad, Calif.; Life Technologies,Gathesburg, Md.) and conceivably even more private sources. It isappreciated that similar enzymes may be developed in the future that areserviceable for end-selection as provided herein. A particularlypreferred topoisomerase I enzyme is a topoisomerase I enzyme of vacciniavirus origin, that has a specific recognition sequence (e.g. 5′ . . .AAGGGG . . . 3′) and has both polynucleotide-nicking activity andpolynucleotide-ligating activity. Due to the specific nicking-activityof this enzyme (cleavage of one strand), internal recognition sites arenot prone to polynucleotide destruction resulting from the nickingactivity (but rather remain annealed) at a temperature that causesdenaturation of a terminal site that has been nicked. Thus for use inend-selection, it is preferable that a nicking site fortopoisomerase-based end-selection be no more than 100 nucleotides from aterminus, more preferably no more than 50 nucleotides from a terminus,more preferably still no more than 25 nucloetides from a terminus, evenmore preferably still no more than 20 nucleotides from a terminus, evenmore preferably still no more than 15 nucleotides from a terminus, evenmore preferably still no more than 10 nucleotides from a terminus, evenmore preferably still no more than 8 nucleotides from a terminus, evenmore preferably still no more than 6 nucleotides from a terminus, andeven more preferably still no more than 4 nucleotides from a terminus.

In a particularly preferred exemplification that is non-limiting yetclearly illustrative, it is appreciated that when a nicking site fortopoisomerase-based end-selection is 4 nucleotides from a terminus,nicking produces a single stranded oligo of 4 bases (in a terminalregion) that can be denatured from its complementary strand in anend-selectable polynucleotide; this provides a sticky end (comprised of4 bases) in a polynucleotide that is serviceable for an ensuing ligationreaction. To accomplish ligation to a cloning vector (preferably anexpression vector), compatible sticky ends can be generated in a cloningvector by any means including by restriction enzyme-based means. Theterminal nucleotides (comprised of 4 terminal bases in this specificexample) in an end-selectable polynucleotide terminus are thus wiselychosen to provide compatibility with a sticky end generated in a cloningvector to which the polynucleotide is to be ligated.

On the other hand, internal nicking of an end-selectable polynucleotide,e.g. 500 bases from a terminus, produces a single stranded oligo of 500bases that is not easily denatured from its complementary strand, butrather is serviceable for repair (e.g. by the same topoisomerase enzymethat produced the nick).

This invention thus provides a method—e.g. that is vacciniatopoisomerase-based &/or type II (or IIS) restriction endonuclease-based&/or type III restriction endonuclease-based &/or nicking enzyme-based(e.g. using N. BstNB I)— for producing a sticky end in a workingpolynucleotide, which end is ligation compatible, and which end can becomprised of at least a 1 base overhang. Preferably such a sticky end iscomprised of at least a 2-base overhang, more preferably such a stickyend is comprised of at least a 3-base overhang, more preferably stillsuch a sticky end is comprised of at least a 4-base overhang, even morepreferably still such a sticky end is comprised of at least a 5-baseoverhang, even more preferably still such a sticky end is comprised ofat least a 6-base overhang. Such a sticky end may also be comprised ofat least a 7-base overhang, or at least an 8-base overhang, or at leasta 9-base overhang, or at least a 10-base overhang, or at least 15-baseoverhang, or at least a 20-base overhang, or at least a 25-baseoverhang, or at least a 30-base overhang. These overhangs can becomprised of any bases, including A, C, G, or T.

It is appreciated that sticky end overhangs introduced usingtopoisomerase or a nicking enzyme (e.g. using N. BstNB I) can bedesigned to be unique in a ligation environment, so as to preventunwanted fragment reassemblies, such as self-dimerizations and otherunwanted concatamerizations.

According to one aspect of this invention, a plurality of sequences(which may but do not necessarily overlap) can be introduced into aterminal region of an end-selectable polynucleotide by the use of anoligo in a polymerase-based reaction. In a relevant, but by no meanslimiting example, such an oligo can be used to provide a preferred 5′terminal region that is serviceable for topoisomerase I-basedend-selection, which oligo is comprised of: a 1-10 base sequence that isconvertible into a sticky end (preferably by a vaccinia topoisomeraseI), a ribosome binding site (i.e. and “RBS”, that is preferablyserviceable for expression cloning), and optional linker sequencefollowed by an ATG start site and a template-specific sequence of 0-100bases (to facilitate annealment to the template in the polymerase-basedreaction). Thus, according to this example, a serviceable oligo (whichmay be termed a forward primer) can have the sequence: 5′[terminalsequence=(N)₁₋₁₀][topoisomerase I site &RBS=AAGGGAGGAG][linker=(N)₁₋₁₀₀][start codon and template-specificsequence=ATG(N)₀₋₁₀₀]3′.

Analogously, in a relevant, but by no means limiting example, an oligocan be used to provide a preferred 3′ terminal region that isserviceable for topoisomerase I-based end-selection, which oligo iscomprised of: a 1-10 base sequence that is convertible into a sticky end(preferably by a vaccinia topoisomerase I), and optional linker sequencefollowed by a template-specific sequence of 0-100 bases (to facilitateannealment to the template in the a polymerase-based reaction). Thus,according to this example, a serviceable oligo (which may be termed areverse primer) can have the sequence: 5′[terminalsequence=(N)₁₋₁₀][topoisomerase Isite=AAGGG][linker=(N)₁₋₁₀₀][template-specific sequence=(N)₀₋₁₀₀]3′.

It is appreciated that, end-selection can be used to distinguish andseparate parental template molecules (e.g. to be subjected tomutagenesis) from progeny molecules (e.g. generated by mutagenesis). Forexample, a first set of primers, lacking in a topoisomerase Irecognition site, can be used to modify the terminal regions of theparental molecules (e.g. in polymerase-based amplification). A differentsecond set of primers (e.g. having a topoisomerase I recognition site)can then be used to generate mutated progeny molecules (e.g. using anypolynucleotide chimerization method, such as interrupted synthesis,template-switching polymerase-based amplification, or interruptedsynthesis; or using saturation mutagenesis; or using any other methodfor introducing a topoisomerase I recognition site into a mutagenizedprogeny molecule as disclosed herein) from the amplified templatemolecules. The use of topoisomerase I-based end-selection can thenfacilitate, not only discernment, but selective topoisomerase I-basedligation of the desired progeny molecules.

Annealment of a second set of primers to thusly amplified parentalmolecules can be facilitated by including sequences in a first set ofprimers (i.e. primers used for amplifying a set parental molecules) thatare similar to a toposiomerase I recognition site, yet different enoughto prevent functional toposiomerase I enzyme recognition. For example,sequences that diverge from the AAGGG site by anywhere from 1 base toall 5 bases can be incorporated into a first set of primers (to be usedfor amplifying the parental templates prior to subjection tomutagenesis). In a specific, but non-limiting aspect, it is thusprovided that a parental molecule can be amplified using the followingexemplary—but by no means limiting—set of forward and reverse primers:

Forward Primer: 5′ CTAGAAGAGAGGAGAAAACCATG(N)₁₀₋₁₀₀ 3′, andReverse Primer: 5′ GATCAAAGGCGCGCCTGCAGG(N)₁₀₋₁₀₀ 3′

According to this specific example of a first set of primers, (N)₁₀₋₁₀₀represents preferably a 10 to 100 nucleotide-long template-specificsequence, more preferably a 10 to 50 nucleotide-long template-specificsequence, more preferably still a 10 to 30 nucleotide-longtemplate-specific sequence, and even more preferably still a 15 to 25nucleotide-long template-specific sequence.

According to a specific, but non-limiting aspect, it is thus providedthat, after this amplification (using a disclosed first set of primerslacking in a true topoisomerase I recognition site), amplified parentalmolecules can then be subjected to mutagenesis using one or more sets offorward and reverse primers that do have a true topoisomerase Irecognition site. In a specific, but non-limiting aspect, it is thusprovided that a parental molecule can be used as templates for thegeneration of a mutagenized progeny molecule using the followingexemplary—but by no means limiting—second set of forward and reverseprimers:

Forward Primer: 5′ CTAGAAGGGAGGAGAAAACCATG 3′ Reverse Primer: 5′GATCAAAGGCGCGCCTGCAGG 3′ (contains Asc I recognition sequence)

It is appreciated that any number of different primers sets notspecifically mentioned can be used as first, second, or subsequent setsof primers for end-selection consistent with this invention. Notice thattype II restriction enzyme sites can be incorporated (e.g. an Asc I sitein the above example). It is provided that, in addition to the othersequences mentioned, the experimentalist can incorporate one or moreN,N,G/T triplets into a serviceable primer in order to subject a workingpolynucleotide to saturation mutagenesis. Summarily, use of a secondand/or subsequent set of primers can achieve dual goals of introducing atopoisomerase I site and of generating mutations in a progenypolynucleotide.

Thus, according to one use provided, a serviceable end-selection markeris an enzyme recognition site that allows an enzyme to cleave (includingnick) a polynucleotide at a specified site, to produce aligation-compatible end upon denaturation of a generated single strandedoligo. Ligation of the produced polynucleotide end can then beaccomplished by the same enzyme (e.g. in the case of vaccinia virustopoisomerase I), or alternatively with the use of a different enzyme.According to one aspect of this invention, any serviceable end-selectionmarkers, whether like (e.g. two vaccinia virus topoisomerase Irecognition sites) or unlike (e.g. a class II restriction enzymerecognition site and a vaccinia virus topoisomerase I recognition site)can be used in combination to select a polynucleotide. Each selectablepolynucleotide can thus have one or more end-selection markers, and theycan be like or unlike end-selection markers. In a particular aspect, aplurality of end-selection markers can be located on one end of apolynucleotide and can have overlapping sequences with each other.

It is important to emphasize that any number of enzymes, whethercurrently in existence or to be developed, can be serviceable inend-selection according to this invention. For example, in a particularaspect of this invention, a nicking enzyme (e.g. N. BstNB I, whichcleaves only one strand at 5′ . . . GAGTCNNNN/N . . . 3′) can be used inconjunction with a source of polynucleotide-ligating activity in orderto achieve end-selection. According to this embodiment, a recognitionsite for N. BstNB I—instead of a recognition site for topoisomeraseI—should be incorporated into an end-selectable polynucleotide (whetherend-selection is used for selection of a mutagenized progeny molecule orwhether end-selection is used apart from any mutagenesis procedure).

It is appreciated that the instantly disclosed end-selection approachusing topoisomerase-based nicking and ligation has several advantagesover previously available selection methods. In sum, this approachallows one to achieve direction cloning (including expression cloning).Specifically, this approach can be used for the achievement of: directligation (i.e. without subjection to a classicrestriction-purification-ligation reaction, that is susceptible to amultitude of potential problems from an initial restriction reaction toa ligation reaction dependent on the use of T4 DNA ligase); separationof progeny molecules from original template molecules (e.g. originaltemplate molecules lack topoisomerase I sites that not introduced untilafter mutagenesis), obviation of the need for size separation steps(e.g. by gel chromatography or by other electrophoretic means or by theuse of size-exclusion membranes), preservation of internal sequences(even when topoisomerase I sites are present), obviation of concernsabout unsuccessful ligation reactions (e.g. dependent on the use of T4DNA ligase, particularly in the presence of unwanted residualrestriction enzyme activity), and facilitated expression cloning(including obviation of frame shift concerns). Concerns about unwantedrestriction enzyme-based cleavages—especially at internal restrictionsites (or even at often unpredictable sites of unwanted star activity)in a working polynucleotide—that are potential sites of destruction of aworking polynucleotide can also be obviated by the instantly disclosedend-selection approach using topoisomerase-based nicking and ligation.

2.11.3. Additional Screening Methods

Peptide Display Methods

The present method can be used to shuffle, by in vitro and/or in vivorecombination by any of the disclosed methods, and in any combination,polynucleotide sequences selected by peptide display methods, wherein anassociated polynucleotide encodes a displayed peptide which is screenedfor a phenotype (e.g., for affinity for a predetermined receptor(ligand).

An increasingly important aspect of bio-pharmaceutical drug developmentand molecular biology is the identification of peptide structures,including the primary amino acid sequences, of peptides orpeptidomimetics that interact with biological macromolecules. One methodof identifying peptides that possess a desired structure or functionalproperty, such as binding to a predetermined biological macromolecule(e.g., a receptor), involves the screening of a large library orpeptides for individual library members which possess the desiredstructure or functional property conferred by the amino acid sequence ofthe peptide.

In addition to direct chemical synthesis methods for generating peptidelibraries, several recombinant DNA methods also have been reported. Onetype involves the display of a peptide sequence, antibody, or otherprotein on the surface of a bacteriophage particle or cell. Generally,in these methods each bacteriophage particle or cell serves as anindividual library member displaying a single species of displayedpeptide in addition to the natural bacteriophage or cell proteinsequences. Each bacteriophage or cell contains the nucleotide sequenceinformation encoding the particular displayed peptide sequence; thus,the displayed peptide sequence can be ascertained by nucleotide sequencedetermination of an isolated library member.

A well-known peptide display method involves the presentation of apeptide sequence on the surface of a filamentous bacteriophage,typically as a fusion with a bacteriophage coat protein. Thebacteriophage library can be incubated with an immobilized,predetermined macromolecule or small molecule (e.g., a receptor) so thatbacteriophage particles which present a peptide sequence that binds tothe immobilized macromolecule can be differentially partitioned fromthose that do not present peptide sequences that bind to thepredetermined macromolecule. The bacteriophage particles (i.e., librarymembers) which are bound to the immobilized macromolecule are thenrecovered and replicated to amplify the selected bacteriophagesub-population for a subsequent round of affinity enrichment and phagereplication. After several rounds of affinity enrichment and phagereplication, the bacteriophage library members that are thus selectedare isolated and the nucleotide sequence encoding the displayed peptidesequence is determined, thereby identifying the sequence(s) of peptidesthat bind to the predetermined macromolecule (e.g., receptor). Suchmethods are further described in PCT patent publications WO 91/17271, WO91/18980, WO 91/19818 and WO 93/08278.

The latter PCT publication describes a recombinant DNA method for thedisplay of peptide ligands that involves the production of a library offusion proteins with each fusion protein composed of a first polypeptideportion, typically comprising a variable sequence, that is available forpotential binding to a predetermined macromolecule, and a secondpolypeptide portion that binds to DNA, such as the DNA vector encodingthe individual fusion protein. When transformed host cells are culturedunder conditions that allow for expression of the fusion protein, thefusion protein binds to the DNA vector encoding it. Upon lysis of thehost cell, the fusion protein/vector DNA complexes can be screenedagainst a predetermined macromolecule in much the same way asbacteriophage particles are screened in the phage-based display system,with the replication and sequencing of the DNA vectors in the selectedfusion protein/vector DNA complexes serving as the basis foridentification of the selected library peptide sequence(s).

Other systems for generating libraries of peptides and like polymershave aspects of both the recombinant and in vitro chemical synthesismethods. In these hybrid methods, cell-free enzymatic machinery isemployed to accomplish the in vitro synthesis of the library members(i.e., peptides or polynucleotides). In one type of method, RNAmolecules with the ability to bind a predetermined protein or apredetermined dye molecule were selected by alternate rounds ofselection and PCR amplification (Tuerk and Gold, 1990; Ellington andSzostak, 1990). A similar technique was used to identify DNA sequenceswhich bind a predetermined human transcription factor (Thiesen and Bach,1990; Beaudry and Joyce, 1992; PCT patent publications WO 92/05258 andWO 92/14843). In a similar fashion, the technique of in vitrotranslation has been used to synthesize proteins of interest and hasbeen proposed as a method for generating large libraries of peptides.These methods which rely upon in vitro translation, generally comprisingstabilized polysome complexes, are described further in PCT patentpublications WO 88/08453, WO 90/05785, WO 90/07003, WO 91/02076, WO91/05058, and WO 92/02536. Applicants have described methods in whichlibrary members comprise a fusion protein having a first polypeptideportion with DNA binding activity and a second polypeptide portionhaving the library member unique peptide sequence; such methods aresuitable for use in cell-free in vitro selection formats, among others.

The displayed peptide sequences can be of varying lengths, typicallyfrom 3-5000 amino acids long or longer, frequently from 5-100 aminoacids long, and often from about 8-15 amino acids long. A library cancomprise library members having varying lengths of displayed peptidesequence, or may comprise library members having a fixed length ofdisplayed peptide sequence. Portions or all of the displayed peptidesequence(s) can be random, pseudorandom, defined set kernal, fixed, orthe like. The present display methods include methods for in vitro andin vivo display of single-chain antibodies, such as nascent scFv onpolysomes or scfv displayed on phage, which enable large-scale screeningof scfv libraries having broad diversity of variable region sequencesand binding specificities.

The present invention also provides random, pseudorandom, and definedsequence framework peptide libraries and methods for generating andscreening those libraries to identify useful compounds (e.g., peptides,including single-chain antibodies) that bind to receptor molecules orepitopes of interest or gene products that modify peptides or RNA in adesired fashion. The random, pseudorandom, and defined sequenceframework peptides are produced from libraries of peptide librarymembers that comprise displayed peptides or displayed single-chainantibodies attached to a polynucleotide template from which thedisplayed peptide was synthesized. The mode of attachment may varyaccording to the specific embodiment of the invention selected, and caninclude encapsulation in a phage particle or incorporation in a cell.

A method of affinity enrichment allows a very large library of peptidesand single-chain antibodies to be screened and the polynucleotidesequence encoding the desired peptide(s) or single-chain antibodies tobe selected. The polynucleotide can then be isolated and shuffled torecombine combinatorially the amino acid sequence of the selectedpeptide(s) (or predetermined portions thereof) or single-chainantibodies (or just VHI, VLI or CDR portions thereof). Using thesemethods, one can identify a peptide or single-chain antibody as having adesired binding affinity for a molecule and can exploit the process ofshuffling to converge rapidly to a desired high-affinity peptide orscfv. The peptide or antibody can then be synthesized in bulk byconventional means for any suitable use (e.g., as a therapeutic ordiagnostic agent).

A significant advantage of the present invention is that no priorinformation regarding an expected ligand structure is required toisolate peptide ligands or antibodies of interest. The peptideidentified can have biological activity, which is meant to include atleast specific binding affinity for a selected receptor molecule and, insome instances, will further include the ability to block the binding ofother compounds, to stimulate or inhibit metabolic pathways, to act as asignal or messenger, to stimulate or inhibit cellular activity, and thelike.

The present invention also provides a method for shuffling a pool ofpolynucleotide sequences selected by affinity screening a library ofpolysomes displaying nascent peptides (including single-chainantibodies) for library members which bind to a predetermined receptor(e.g., a mammalian proteinaceous receptor such as, for example, apeptidergic hormone receptor, a cell surface receptor, an intracellularprotein which binds to other protein(s) to form intracellular proteincomplexes such as hetero-dimers and the like) or epitope (e.g., animmobilized protein, glycoprotein, oligosaccharide, and the like).

Polynucleotide sequences selected in a first selection round (typicallyby affinity selection for binding to a receptor (e.g., a ligand)) by anyof these methods are pooled and the pool(s) is/are shuffled by in vitroand/or in vivo recombination to produce a shuffled pool comprising apopulation of recombined selected polynucleotide sequences. Therecombined selected polynucleotide sequences are subjected to at leastone subsequent selection round. The polynucleotide sequences selected inthe subsequent selection round(s) can be used directly, sequenced,and/or subjected to one or more additional rounds of shuffling andsubsequent selection. Selected sequences can also be back-crossed withpolynucleotide sequences encoding neutral sequences (i.e., havinginsubstantial functional effect on binding), such as for example byback-crossing with a wild-type or naturally-occurring sequencesubstantially identical to a selected sequence to produce native-likefunctional peptides, which may be less immunogenic. Generally, duringback-crossing subsequent selection is applied to retain the property ofbinding to the predetermined receptor (ligand).

Prior to or concomitant with the shuffling of selected sequences, thesequences can be mutagenized. In one embodiment, selected librarymembers are cloned in a prokaryotic vector (e.g., plasmid, phagemid, orbacteriophage) wherein a collection of individual colonies (or plaques)representing discrete library members are produced. Individual selectedlibrary members can then be manipulated (e.g., by site-directedmutagenesis, cassette mutagenesis, chemical mutagenesis, PCRmutagenesis, and the like) to generate a collection of library membersrepresenting a kernal of sequence diversity based on the sequence of theselected library member. The sequence of an individual selected librarymember or pool can be manipulated to incorporate random mutation,pseudorandom mutation, defined kernal mutation (i.e., comprising variantand invariant residue positions and/or comprising variant residuepositions which can comprise a residue selected from a defined subset ofamino acid residues), codon-based mutation, and the like, eithersegmentally or over the entire length of the individual selected librarymember sequence. The mutagenized selected library members are thenshuffled by in vitro and/or in vivo recombinatorial shuffling asdisclosed herein.

The invention also provides peptide libraries comprising a plurality ofindividual library members of the invention, wherein (1) each individuallibrary member of said plurality comprises a sequence produced byshuffling of a pool of selected sequences, and (2) each individuallibrary member comprises a variable peptide segment sequence orsingle-chain antibody segment sequence which is distinct from thevariable peptide segment sequences or single-chain antibody sequences ofother individual library members in said plurality (although somelibrary members may be present in more than one copy per library due touneven amplification, stochastic probability, or the like).

The invention also provides a product-by-process, wherein selectedpolynucleotide sequences having (or encoding a peptide having) apredetermined binding specificity are formed by the process of: (1)screening a displayed peptide or displayed single-chain antibody libraryagainst a predetermined receptor (e.g., ligand) or epitope (e.g.,antigen macromolecule) and identifying and/or enriching library memberswhich bind to the predetermined receptor or epitope to produce a pool ofselected library members, (2) shuffling by recombination the selectedlibrary members (or amplified or cloned copies thereof) which binds thepredetermined epitope and has been thereby isolated and/or enriched fromthe library to generate a shuffled library, and (3) screening theshuffled library against the predetermined receptor (e.g., ligand) orepitope (e.g., antigen macromolecule) and identifying and/or enrichingshuffled library members which bind to the predetermined receptor orepitope to produce a pool of selected shuffled library members.

Antibody Display and Screening Methods

The present method can be used to shuffle, by in vitro and/or in vivorecombination by any of the disclosed methods, and in any combination,polynucleotide sequences selected by antibody display methods, whereinan associated polynucleotide encodes a displayed antibody which isscreened for a phenotype (e.g., for affinity for binding a predeterminedantigen (ligand).

Various molecular genetic approaches have been devised to capture thevast immunological repertoire represented by the extremely large numberof distinct variable regions which can be present in immunoglobulinchains. The naturally-occurring germ line immunoglobulin heavy chainlocus is composed of separate tandem arrays of variable segment geneslocated upstream of a tandem array of diversity segment genes, which arethemselves located upstream of a tandem array of joining (i) regiongenes, which are located upstream of the constant region genes. During Blymphocyte development, V-D-J rearrangement occurs wherein a heavy chainvariable region gene (VH) is formed by rearrangement to form a fused Dsegment followed by rearrangement with a V segment to form a V-D-Jjoined product gene which, if productively rearranged, encodes afunctional variable region (VH) of a heavy chain. Similarly, light chainloci rearrange one of several V segments with one of several J segmentsto form a gene encoding the variable region (VL) of a light chain.

The vast repertoire of variable regions possible in immunoglobulinsderives in part from the numerous combinatorial possibilities of joiningV and i segments (and, in the case of heavy chain loci, D segments)during rearrangement in B cell development. Additional sequencediversity in the heavy chain variable regions arises from non-uniformrearrangements of the D segments during V-D-J joining and from N regionaddition. Further, antigen-selection of specific B cell clones selectsfor higher affinity variants having non-germline mutations in one orboth of the heavy and light chain variable regions; a phenomenonreferred to as “affinity maturation” or “affinity sharpening”.Typically, these “affinity sharpening” mutations cluster in specificareas of the variable region, most commonly in thecomplementarity-determining regions (CDRs).

In order to overcome many of the limitations in producing andidentifying high-affinity immunoglobulins through antigen-stimulated Bcell development (i.e., immunization), various prokaryotic expressionsystems have been developed that can be manipulated to producecombinatorial antibody libraries which may be screened for high-affinityantibodies to specific antigens. Recent advances in the expression ofantibodies in Escherichia coli and bacteriophage systems (see“alternative peptide display methods”, infra) have raised thepossibility that virtually any specificity can be obtained by eithercloning antibody genes from characterized hybridomas or by de novoselection using antibody gene libraries (e.g., from Ig cDNA).

Combinatorial libraries of antibodies have been generated inbacteriophage lambda expression systems which may be screened asbacteriophage plaques or as colonies of lysogens (Huse et al, 1989);Caton and Koprowski, 1990; Mullinax et al, 1990; Persson et al, 1991).Various embodiments of bacteriophage antibody display libraries andlambda phage expression libraries have been described (Kang et al, 1991;Clackson et al, 1991; McCafferty et al, 1990; Burton et al, 1991;Hoogenboom et al, 1991; Chang et al, 1991; Breitling et al, 1991; Markset al, 1991, p. 581; Barbas et al, 1992; Hawkins and Winter, 1992; Markset al, 1992, p. 779; Marks et al, 1992, p. 16007; and Lowman et al,1991; Lerner et al, 1992; all incorporated herein by reference).Typically, a bacteriophage antibody display library is screened with areceptor (e.g., polypeptide, carbohydrate, glycoprotein, nucleic acid)that is immobilized (e.g., by covalent linkage to a chromatography resinto enrich for reactive phage by affinity chromatography) and/or labeled(e.g., to screen plaque or colony lifts).

One particularly advantageous approach has been the use of so-calledsingle-chain fragment variable (scfv) libraries (Marks et al, 1992, p.779; Winter and Milstein, 1991; Clackson et al, 1991; Marks et al, 1991,p. 581; Chaudhary et al, 1990; Chiswell et al, 1992; McCafferty et al,1990; and Huston et al, 1988). Various embodiments of scfv librariesdisplayed on bacteriophage coat proteins have been described.

Beginning in 1988, single-chain analogues of Fv fragments and theirfusion proteins have been reliably generated by antibody engineeringmethods. The first step generally involves obtaining the genes encodingVH and VL domains with desired binding properties; these V genes may beisolated from a specific hybridoma cell line, selected from acombinatorial V-gene library, or made by V gene synthesis. Thesingle-chain Fv is formed by connecting the component V genes with anoligonucleotide that encodes an appropriately designed linker peptide,such as (Gly-Gly-Gly-Gly-Ser)₃ or equivalent linker peptide(s). Thelinker bridges the C-terminus of the first V region and N-terminus ofthe second, ordered as either VH-linker-VL or VL-linker-VH. Inprinciple, the scfv binding site can faithfully replicate both theaffinity and specificity of its parent antibody combining site.

Thus, scfv fragments are comprised of VH and VL domains linked into asingle polypeptide chain by a flexible linker peptide. After the scfvgenes are assembled, they are cloned into a phagemid and expressed atthe tip of the M13 phage (or similar filamentous bacteriophage) asfusion proteins with the bacteriophage PIII (gene 3) coat protein.Enriching for phage expressing an antibody of interest is accomplishedby panning the recombinant phage displaying a population scfv forbinding to a predetermined epitope (e.g., target antigen, receptor).

The linked polynucleotide of a library member provides the basis forreplication of the library member after a screening or selectionprocedure, and also provides the basis for the determination, bynucleotide sequencing, of the identity of the displayed peptide sequenceor VH and VL amino acid sequence. The displayed peptide (s) orsingle-chain antibody (e.g., scfv) and/or its VH and VL domains or theirCDRs can be cloned and expressed in a suitable expression system. Oftenpolynucleotides encoding the isolated VH and VL domains will be ligatedto polynucleotides encoding constant regions (CH and CL) to formpolynucleotides encoding complete antibodies (e.g., chimeric orfully-human), antibody fragments, and the like. Often polynucleotidesencoding the isolated CDRs will be grafted into polynucleotides encodinga suitable variable region framework (and optionally constant regions)to form polynucleotides encoding complete antibodies (e.g., humanized orfully-human), antibody fragments, and the like. Antibodies can be usedto isolate preparative quantities of the antigen by immunoaffinitychromatography. Various other uses of such antibodies are to diagnoseand/or stage disease (e.g., neoplasia) and for therapeutic applicationto treat disease, such as for example: neoplasia, autoimmune disease,AIDS, cardiovascular disease, infections, and the like.

Various methods have been reported for increasing the combinatorialdiversity of a scfv library to broaden the repertoire of binding species(idiotype spectrum) The use of PCR has permitted the variable regions tobe rapidly cloned either from a specific hybridoma source or as a genelibrary from non-immunized cells, affording combinatorial diversity inthe assortment of VH and VL cassettes which can be combined.Furthermore, the VH and VL cassettes can themselves be diversified, suchas by random, pseudorandom, or directed mutagenesis. Typically, VH andVL cassettes are diversified in or near the complementarity-determiningregions (CDRS), often the third CDR, CDR3. Enzymatic inverse PCRmutagenesis has been shown to be a simple and reliable method forconstructing relatively large libraries of scfv site-directed hybrids(Stemmer et al, 1993), as has error-prone PCR and chemical mutagenesis(Deng et al, 1994). Riechmann (Riechmann et al, 1993) showedsemi-rational design of an antibody scfv fragment using site-directedrandomization by degenerate oligonucleotide PCR and subsequent phagedisplay of the resultant scfv hybrids. Barbas (Barbas et al, 1992)attempted to circumvent the problem of limited repertoire sizesresulting from using biased variable region sequences by randomizing thesequence in a synthetic CDR region of a human tetanus toxoid-bindingFab.

CDR randomization has the potential to create approximately 1×10²⁰ CDRsfor the heavy chain CDR3 alone, and a roughly similar number of variantsof the heavy chain CDR1 and CDR2, and light chain CDR1-3 variants. Takenindividually or together, the combination possibilities of CDRrandomization of heavy and/or light chains requires generating aprohibitive number of bacteriophage clones to produce a clone libraryrepresenting all possible combinations, the vast majority of which willbe non-binding. Generation of such large numbers of primarytransformants is not feasible with current transformation technology andbacteriophage display systems. For example, Barbas (Barbas et al, 1992)only generated 5×10⁷ transformants, which represents only a tinyfraction of the potential diversity of a library of thoroughlyrandomized CDRS.

Despite these substantial limitations, bacteriophage display of scfvhave already yielded a variety of useful antibodies and antibody fusionproteins. A bispecific single chain antibody has been shown to mediateefficient tumor cell lysis (Gruber et al, 1994). Intracellularexpression of an anti-Rev scfv has been shown to inhibit HW-1 virusreplication in vitro (Duan et al, 1994), and intracellular expression ofan anti-p2lrar, scfv has been shown to inhibit meiotic maturation ofXenopus oocytes (Biocca et al, 1993). Recombinant scfv which can be usedto diagnose HIV infection have also been reported, demonstrating thediagnostic utility of scfv (Lilley et al, 1994). Fusion proteins whereinan scFv is linked to a second polypeptide, such as a toxin orfibrinolytic activator protein, have also been reported (Holvost et al,1992; Nicholls et al, 1993).

If it were possible to generate scfv libraries having broader antibodydiversity and overcoming many of the limitations of conventional CDRmutagenesis and randomization methods which can cover only a very tinyfraction of the potential sequence combinations, the number and qualityof scfv antibodies suitable for therapeutic and diagnostic use could bevastly improved. To address this, the in vitro and in vivo shufflingmethods of the invention are used to recombine CDRs which have beenobtained (typically via PCR amplification or cloning) from nucleic acidsobtained from selected displayed antibodies. Such displayed antibodiescan be displayed on cells, on bacteriophage particles, on polysomes, orany suitable antibody display system wherein the antibody is associatedwith its encoding nucleic acid(s). In a variation, the CDRs areinitially obtained from mRNA (or cDNA) from antibody-producing cells(e.g., plasma cells/splenocytes from an immunized wild-type mouse, ahuman, or a transgenic mouse capable of making a human antibody as in WO92/03918, WO 93/12227, and WO 94/25585), including hybridomas derivedtherefrom.

Polynucleotide sequences selected in a first selection round (typicallyby affinity selection for displayed antibody binding to an antigen(e.g., a ligand) by any of these methods are pooled and the pool(s)is/are shuffled by in vitro and/or in vivo recombination, especiallyshuffling of CDRs (typically shuffling heavy chain CDRs with other heavychain CDRs and light chain CDRs with other light chain CDRs) to producea shuffled pool comprising a population of recombined selectedpolynucleotide sequences. The recombined selected polynucleotidesequences are expressed in a selection format as a displayed antibodyand subjected to at least one subsequent selection round. Thepolynucleotide sequences selected in the subsequent selection round(s)can be used directly, sequenced, and/or subjected to one or moreadditional rounds of shuffling and subsequent selection until anantibody of the desired binding affinity is obtained. Selected sequencescan also be back-crossed with polynucleotide sequences encoding neutralantibody framework sequences (i.e., having insubstantial functionaleffect on antigen binding), such as for example by back-crossing with ahuman variable region framework to produce human-like sequenceantibodies. Generally, during back-crossing subsequent selection isapplied to retain the property of binding to the predetermined antigen.

Alternatively, or in combination with the noted variations, the valencyof the target epitope may be varied to control the average bindingaffinity of selected scfv library members. The target epitope can bebound to a surface or substrate at varying densities, such as byincluding a competitor epitope, by dilution, or by other method known tothose in the art. A high density (valency) of predetermined epitope canbe used to enrich for scfv library members which have relatively lowaffinity, whereas a low density (valency) can preferentially enrich forhigher affinity scfv library members.

For generating diverse variable segments, a collection of syntheticoligonucleotides encoding random, pseudorandom, or a defined sequencekernal set of peptide sequences can be inserted by ligation into apredetermined site (e.g., a CDR). Similarly, the sequence diversity ofone or more CDRs of the single-chain antibody cassette(s) can beexpanded by mutating the CDR(s) with site-directed mutagenesis,CDR-replacement, and the like. The resultant DNA molecules can bepropagated in a host for cloning and amplification prior to shuffling,or can be used directly (i.e., may avoid loss of diversity which mayoccur upon propagation in a host cell) and the selected library memberssubsequently shuffled.

Displayed peptide/polynucleotide complexes (library members) whichencode a variable segment peptide sequence of interest or a single-chainantibody of interest are selected from the library by an affinityenrichment technique. This is accomplished by means of a immobilizedmacromolecule or epitope specific for the peptide sequence of interest,such as a receptor, other macromolecule, or other epitope species.Repeating the affinity selection procedure provides an enrichment oflibrary members encoding the desired sequences, which may then beisolated for pooling and shuffling, for sequencing, and/or for furtherpropagation and affinity enrichment.

The library members without the desired specificity are removed bywashing. The degree and stringency of washing required will bedetermined for each peptide sequence or single-chain antibody ofinterest and the immobilized predetermined macromolecule or epitope. Acertain degree of control can be exerted over the bindingcharacteristics of the nascent peptide/DNA complexes recovered byadjusting the conditions of the binding incubation and the subsequentwashing. The temperature, pH, ionic strength, divalent cationsconcentration, and the volume and duration of the washing will selectfor nascent peptide/DNA complexes within particular ranges of affinityfor the immobilized macromolecule. Selection based on slow dissociationrate, which is usually predictive of high affinity, is often the mostpractical route. This may be done either by continued incubation in thepresence of a saturating amount of free predetermined macromolecule, orby increasing the volume, number, and length of the washes. In eachcase, the rebinding of dissociated nascent peptide/DNA or peptide/RNAcomplex is prevented, and with increasing time, nascent peptide/DNA orpeptide/RNA complexes of higher and higher affinity are recovered.

Additional modifications of the binding and washing procedures may beapplied to find peptides with special characteristics. The affinities ofsome peptides are dependent on ionic strength or cation concentration.This is a useful characteristic for peptides that will be used inaffinity purification of various proteins when gentle conditions forremoving the protein from the peptides are required.

One variation involves the use of multiple binding targets (multipleepitope species, multiple receptor species), such that a scfv librarycan be simultaneously screened for a multiplicity of scfv which havedifferent binding specificities. Given that the size of a scfv libraryoften limits the diversity of potential scfv sequences, it is typicallydesirable to us scfv libraries of as large a size as possible. The timeand economic considerations of generating a number of very largepolysome scFv-display libraries can become prohibitive. To avoid thissubstantial problem, multiple predetermined epitope species (receptorspecies) can be concomitantly screened in a single library, orsequential screening against a number of epitope species can be used. Inone variation, multiple target epitope species, each encoded on aseparate bead (or subset of beads), can be mixed and incubated with apolysome-display scfv library under suitable binding conditions. Thecollection of beads, comprising multiple epitope species, can then beused to isolate, by affinity selection, scfv library members. Generally,subsequent affinity screening rounds can include the same mixture ofbeads, subsets thereof, or beads containing only one or two individualepitope species. This approach affords efficient screening, and iscompatible with laboratory automation, batch processing, and highthroughput screening methods.

A variety of techniques can be used in the present invention todiversify a peptide library or single-chain antibody library, or todiversify, prior to or concomitant with shuffling, around variablesegment peptides found in early rounds of panning to have sufficientbinding activity to the predetermined macromolecule or epitope. In oneapproach, the positive selected peptide/polynucleotide complexes (thoseidentified in an early round of affinity enrichment) are sequenced todetermine the identity of the active peptides. Oligonucleotides are thensynthesized based on these active peptide sequences, employing a lowlevel of all bases incorporated at each step to produce slightvariations of the primary oligonucleotide sequences. This mixture of(slightly) degenerate oligonucleotides is then cloned into the variablesegment sequences at the appropriate locations. This method producessystematic, controlled variations of the starting peptide sequences,which can then be shuffled. It requires, however, that individualpositive nascent peptide/polynucleotide complexes be sequenced beforemutagenesis, and thus is useful for expanding the diversity of smallnumbers of recovered complexes and selecting variants having higherbinding affinity and/or higher binding specificity. In a variation,mutagenic PCR amplification of positive selected peptide/polynucleotidecomplexes (especially of the variable region sequences, theamplification products of which are shuffled in vitro and/or in vivo andone or more additional rounds of screening is done prior to sequencing.The same general approach can be employed with single-chain antibodiesin order to expand the diversity and enhance the bindingaffinity/specificity, typically by diversifying CDRs or adjacentframework regions prior to or concomitant with shuffling. If desired,shuffling reactions can be spiked with mutagenic oligonucleotidescapable of in vitro recombination with the selected library members canbe included. Thus, mixtures of synthetic oligonucleotides and PCRproduced polynucleotides (synthesized by error-prone or high-fidelitymethods) can be added to the in vitro shuffling mix and be incorporatedinto resulting shuffled library members (shufflants).

The present invention of shuffling enables the generation of a vastlibrary of CDR-variant single-chain antibodies. One way to generate suchantibodies is to insert synthetic CDRs into the single-chain antibodyand/or CDR randomization prior to or concomitant with shuffling. Thesequences of the synthetic CDR cassettes are selected by referring toknown sequence data of human CDR and are selected in the discretion ofthe practitioner according to the following guidelines: synthetic CDRswill have at least 40 percent positional sequence identity to known CDRsequences, and preferably will have at least 50 to 70 percent positionalsequence identity to known CDR sequences. For example, a collection ofsynthetic CDR sequences can be generated by synthesizing a collection ofoligonucleotide sequences on the basis of naturally-occurring human CDRsequences listed in Kabat (Kabat et al, 1991); the pool (s) of syntheticCDR sequences are calculated to encode CDR peptide sequences having atleast 40 percent sequence identity to at least one knownnaturally-occurring human CDR sequence. Alternatively, a collection ofnaturally-occurring CDR sequences may be compared to generate consensussequences so that amino acids used at a residue position frequently(i.e., in at least 5 percent of known CDR sequences) are incorporatedinto the synthetic CDRs at the corresponding position(s). Typically,several (e.g., 3 to about 50) known CDR sequences are compared andobserved natural sequence variations between the known CDRs aretabulated, and a collection of oligonucleotides encoding CDR peptidesequences encompassing all or most permutations of the observed naturalsequence variations is synthesized. For example but not for limitation,if a collection of human VH CDR sequences have carboxy-terminal aminoacids which are either Tyr, Val, Phe, or Asp, then the pool(s) ofsynthetic CDR oligonucleotide sequences are designed to allow thecarboxy-terminal CDR residue to be any of these amino acids. In someembodiments, residues other than those which naturally-occur at aresidue position in the collection of CDR sequences are incorporated:conservative amino acid substitutions are frequently incorporated and upto 5 residue positions may be varied to incorporate non-conservativeamino acid substitutions as compared to known naturally-occurring CDRsequences. Such CDR sequences can be used in primary library members(prior to first round screening) and/or can be used to spike in vitroshuffling reactions of selected library member sequences. Constructionof such pools of defined and/or degenerate sequences will be readilyaccomplished by those of ordinary skill in the art.

The collection of synthetic CDR sequences comprises at least one memberthat is not known to be a naturally-occurring CDR sequence. It is withinthe discretion of the practitioner to include or not include a portionof random or pseudorandom sequence corresponding to N region addition inthe heavy chain CDR; the N region sequence ranges from 1 nucleotide toabout 4 nucleotides occurring at V-D and D-J junctions. A collection ofsynthetic heavy chain CDR sequences comprises at least about 100 uniqueCDR sequences, typically at least about 1,000 unique CDR sequences,preferably at least about 10,000 unique CDR sequences, frequently morethan 50,000 unique CDR sequences; however, usually not more than about1×106 unique CDR sequences are included in the collection, althoughoccasionally 1×107 to 1×108 unique CDR sequences are present, especiallyif conservative amino acid substitutions are permitted at positionswhere the conservative amino acid substituent is not present or is rare(i.e., less than 0.1 percent) in that position in naturally-occurringhuman CDRS. In general, the number of unique CDR sequences included in alibrary should not exceed the expected number of primary transformantsin the library by more than a factor of 10. Such single-chain antibodiesgenerally bind of about at least 1×10 M-1, preferably with an affinityof about at least 5×10⁷ M-1, more preferably with an affinity of atleast 1×10⁸ M-1 to 1×10⁹ M-1 or more, sometimes up to 1×10¹⁰ M-1 ormore. Frequently, the predetermined antigen is a human protein, such asfor example a human cell surface antigen (e.g., CD4, CD8, IL-2 receptor,EGF receptor, PDGF receptor), other human biological macromolecule(e.g., thrombomodulin, protein C, carbohydrate antigen, sialyl Lewisantigen, Lselectin), or nonhuman disease associated macromolecule (e.g.,bacterial LPS, virion capsid protein or envelope glycoprotein) and thelike.

High affinity single-chain antibodies of the desired specificity can beengineered and expressed in a variety of systems. For example, scfv havebeen produced in plants (Firek et al, 1993) and can be readily made inprokaryotic systems (Owens and Young, 1994; Johnson and Bird, 1991).Furthermore, the single-chain antibodies can be used as a basis forconstructing whole antibodies or various fragments thereof(Kettleborough et al, 1994). The variable region encoding sequence maybe isolated (e.g., by PCR amplification or subcloning) and spliced to asequence encoding a desired human constant region to encode a humansequence antibody more suitable for human therapeutic uses whereimmunogenicity is preferably minimized. The polynucleotide(s) having theresultant fully human encoding sequence(s) can be expressed in a hostcell (e.g., from an expression vector in a mammalian cell) and purifiedfor pharmaceutical formulation.

The DNA expression constructs will typically include an expressioncontrol DNA sequence operably linked to the coding sequences, includingnaturally-associated or heterologous promoter regions. Preferably, theexpression control sequences will be eukaryotic promoter systems invectors capable of transforming or transfecting eukaryotic host cells.Once the vector has been incorporated into the appropriate host, thehost is maintained under conditions suitable for high level expressionof the nucleotide sequences, and the collection and purification of themutant “engineered” antibodies.

As stated previously, the DNA sequences will be expressed in hosts afterthe sequences have been operably linked to an expression controlsequence (i.e., positioned to ensure the transcription and translationof the structural gene). These expression vectors are typicallyreplicable in the host organisms either as episomes or as an integralpart of the host chromosomal DNA. Commonly, expression vectors willcontain selection markers, e.g., tetracycline or neomycin, to permitdetection of those cells transformed with the desired DNA sequences(see, e.g., U.S. Pat. No. 4,704,362, which is incorporated herein byreference).

In addition to eukaryotic microorganisms such as yeast, mammalian tissuecell culture may also be used to produce the polypeptides of the presentinvention (see Winnacker, 1987), which is incorporated herein byreference). Eukaryotic cells are actually preferred, because a number ofsuitable host cell lines capable of secreting intact immunoglobulinshave been developed in the art, and include the CHO cell lines, variousCOS cell lines, HeLa cells, and myeloma cell lines, but preferablytransformed Bcells or hybridomas. Expression vectors for these cells caninclude expression control sequences, such as an origin of replication,a promoter, an enhancer (Queen et al, 1986), and necessary processinginformation sites, such as ribosome binding sites, RNA splice sites,polyadenylation sites, and transcriptional terminator sequences.Preferred expression control sequences are promoters derived fromimmunoglobulin genes, cytomegalovirus, SV40, Adenovirus, BovinePapilloma Virus, and the like.

Eukaryotic DNA transcription can be increased by inserting an enhancersequence into the vector. Enhancers are cis-acting sequences of between10 to 300 bp that increase transcription by a promoter. Enhancers caneffectively increase transcription when either 51 or 31 to thetranscription unit. They are also effective if located within an intronor within the coding sequence itself. Typically, viral enhancers areused, including SV40 enhancers, cytomegalovirus enhancers, polyomaenhancers, and adenovirus enhancers. Enhancer sequences from mammaliansystems are also commonly used, such as the mouse immunoglobulin heavychain enhancer.

Mammalian expression vector systems will also typically include aselectable marker gene. Examples of suitable markers include, thedihydrofolate reductase gene (DHFR), the thymidine kinase gene (TK), orprokaryotic genes conferring drug resistance. The first two marker genesprefer the use of mutant cell lines that lack the ability to growwithout the addition of thymidine to the growth medium. Transformedcells can then be identified by their ability to grow onnon-supplemented media. Examples of prokaryotic drug resistance genesuseful as markers include genes conferring resistance to G418,mycophenolic acid and hygromycin.

The vectors containing the DNA segments of interest can be transferredinto the host cell by well-known methods, depending on the type ofcellular host. For example, calcium chloride transfection is commonlyutilized for prokaryotic cells, whereas calcium phosphate treatment,lipofection, or electroporation may be used for other cellular hosts.Other methods used to transform mammalian cells include the use ofPolybrene, protoplast fusion, liposomes, electroporation, andmicro-injection (see, generally, Sambrook et al, 1982 and 1989).

Once expressed, the antibodies, individual mutated immunoglobulinchains, mutated antibody fragments, and other immunoglobulinpolypeptides of the invention can be purified according to standardprocedures of the art, including ammonium sulfate precipitation,fraction column chromatography, gel electrophoresis and the like (see,generally, Scopes, 1982). Once purified, partially or to homogeneity asdesired, the polypeptides may then be used therapeutically or indeveloping and performing assay procedures, immunofluorescent stainings,and the like (see, generally, Lefkovits and Pernis, 1979 and 1981;Lefkovits, 1997).

The antibodies generated by the method of the present invention can beused for diagnosis and therapy. By way of illustration and notlimitation, they can be used to treat cancer, autoimmune diseases, orviral infections. For treatment of cancer, the antibodies will typicallybind to an antigen expressed preferentially on cancer cells, such aserbB-2, CEA, CD33, and many other antigens and binding members wellknown to those skilled in the art.

Two-Hybrid Based Screening Assays

Shuffling can also be used to recombinatorially diversify a pool ofselected library members obtained by screening a two-hybrid screeningsystem to identify library members which bind a predeterminedpolypeptide sequence. The selected library members are pooled andshuffled by in vitro and/or in vivo recombination. The shuffled pool canthen be screened in a yeast two hybrid system to select library memberswhich bind said predetermined polypeptide sequence (e.g., and SH2domain) or which bind an alternate predetermined polypeptide sequence(e.g., an SH2 domain from another protein species).

An approach to identifying polypeptide sequences which bind to apredetermined polypeptide sequence has been to use a so-called“two-hybrid” system wherein the predetermined polypeptide sequence ispresent in a fusion protein (Chien et al, 1991). This approachidentifies protein-protein interactions in vivo through reconstitutionof a transcriptional activator (Fields and Song, 1989), the yeast Gal4transcription protein. Typically, the method is based on the propertiesof the yeast Gal4 protein, which consists of separable domainsresponsible for DNA-binding and transcriptional activation.Polynucleotides encoding two hybrid proteins, one consisting of theyeast Gal4 DNA-binding domain fused to a polypeptide sequence of a knownprotein and the other consisting of the Gal4 activation domain fused toa polypeptide sequence of a second protein, are constructed andintroduced into a yeast host cell. Intermolecular binding between thetwo fusion proteins reconstitutes the Gal4 DNA-binding domain with theGal4 activation domain, which leads to the transcriptional activation ofa reporter gene (e.g., lacz, HIS3) which is operably linked to a Gal4binding site. Typically, the two-hybrid method is used to identify novelpolypeptide sequences which interact with a known protein (Silver andHunt, 1993; Durfee et al, 1993; Yang et al, 1992; Luban et al, 1993;Hardy et al, 1992; Bartel et al, 1993; and Vojtek et al, 1993). However,variations of the two-hybrid method have been used to identify mutationsof a known protein that affect its binding to a second known protein (Liand Fields, 1993; Lalo et al, 1993; Jackson et al, 1993; and Madura etal, 1993). Two-hybrid systems have also been used to identifyinteracting structural domains of two known proteins (Bardwell et al,1993; Chakrabarty et al, 1992; Staudinger et al, 1993; and Milne andWeaver 1993) or domains responsible for oligomerization of a singleprotein (Iwabuchi et al, 1993; Bogerd et al, 1993). Variations oftwo-hybrid systems have been used to study the in vivo activity of aproteolytic enzyme (Dasmahapatra et al, 1992). Alternatively, an E.coli/BCCP interactive screening system (Germino et al, 1993; Guarente,1993) can be used to identify interacting protein sequences (i.e.,protein sequences which heterodimerize or form higher orderheteromultimers). Sequences selected by a two-hybrid system can bepooled and shuffled and introduced into a two-hybrid system for one ormore subsequent rounds of screening to identify polypeptide sequenceswhich bind to the hybrid containing the predetermined binding sequence.The sequences thus identified can be compared to identify consensussequence(s) and consensus sequence kernals.

In general, standard techniques of recombination DNA technology aredescribed in various publications (e.g. Sambrook et al, 1989; Ausubel etal, 1987; and Berger and Kimmel, 1987); each of which is incorporatedherein in its entirety by reference. Polynucleotide modifying enzymeswere used according to the manufacturer's recommendations.Oligonucleotides were synthesized on an Applied Biosystems Inc. Model394 DNA synthesizer using ABI chemicals. If desired, PCR amplimers foramplifying a predetermined DNA sequence may be selected at thediscretion of the practitioner.

One microgram samples of template DNA are obtained and treated with U.V.light to cause the formation of dimers, including TT dimers,particularly purine dimers. U.V. exposure is limited so that only a fewphotoproducts are generated per gene on the template DNA sample.Multiple samples are treated with U.V. light for varying periods of timeto obtain template DNA samples with varying numbers of dimers from U.V.exposure.

A random priming kit which utilizes a non-proofreading polymease (forexample, Prime-It II Random Primer Labeling kit by Stratagene CloningSystems) is utilized to generate different size polynucleotides bypriming at random sites on templates which are prepared by U.V. light(as described above) and extending along the templates. The primingprotocols such as described in the Prime-It II Random Primer Labelingkit may be utilized to extend the primers. The dimers formed by U.V.exposure serve as a roadblock for the extension by the non-proofreadingpolymerase. Thus, a pool of random size polynucleotides is present afterextension with the random primers is finished.

The present invention is further directed to a method for generating aselected mutant polynucleotide sequence (or a population of selectedpolynucleotide sequences) typically in the form of amplified and/orcloned polynucleotides, whereby the selected polynucleotide sequences(s)possess at least one desired phenotypic characteristic (e.g., encodes apolypeptide, promotes transcription of linked polynucleotides, binds aprotein, and the like) which can be selected for. One method foridentifying hybrid polypeptides that possess a desired structure orfunctional property, such as binding to a predetermined biologicalmacromolecule (e.g., a receptor), involves the screening of a largelibrary of polypeptides for individual library members which possess thedesired structure or functional property conferred by the amino acidsequence of the polypeptide.

In one embodiment, the present invention provides a method forgenerating libraries of displayed polypeptides or displayed antibodiessuitable for affinity interaction screening or phenotypic screening. Themethod comprises (1) obtaining a first plurality of selected librarymembers comprising a displayed polypeptide or displayed antibody and anassociated polynucleotide encoding said displayed polypeptide ordisplayed antibody, and obtaining said associated polynucleotides orcopies thereof wherein said associated polynucleotides comprise a regionof substantially identical sequences, optimally introducing mutationsinto said polynucleotides or copies, (2) pooling the polynucleotides orcopies, (3) producing smaller or shorter polynucleotides by interruptinga random or particularized priming and synthesis process or anamplification process, and (4) performing amplification, preferably PCRamplification, and optionally mutagenesis to homologously recombine thenewly synthesized polynucleotides.

It is a particularly preferred object of the invention to provide aprocess for producing hybrid polynucleotides which express a usefulhybrid polypeptide by a series of steps comprising:

(a) producing polynucleotides by interrupting a polynucleotideamplification or synthesis process with a means for blocking orinterrupting the amplification or synthesis process and thus providing aplurality of smaller or shorter polynucleotides due to the replicationof the polynucleotide being in various stages of completion;

(b) adding to the resultant population of single- or double-strandedpolynucleotides one or more single- or double-stranded oligonucleotides,wherein said added oligonucleotides comprise an area of identity in anarea of heterology to one or more of the single- or double-strandedpolynucleotides of the population;

(c) denaturing the resulting single- or double-stranded oligonucleotidesto produce a mixture of single-stranded polynucleotides, optionallyseparating the shorter or smaller polynucleotides into pools ofpolynucleotides having various lengths and further optionally subjectingsaid polynucleotides to a PCR procedure to amplify one or moreoligonucleotides comprised by at least one of said polynucleotide pools;

(d) incubating a plurality of said polynucleotides or at least one poolof said polynucleotides with a polymerase under conditions which resultin annealing of said single-stranded polynucleotides at regions ofidentity between the single-stranded polynucleotides and thus forming ofa mutagenized double-stranded polynucleotide chain;

(e) optionally repeating steps (c) and (d);

(f) expressing at least one hybrid polypeptide from said polynucleotidechain, or chains; and

(g) screening said at least one hybrid polypeptide for a usefulactivity.

In a preferred aspect of the invention, the means for blocking orinterrupting the amplification or synthesis process is by utilization ofU.V. light, DNA adducts, DNA binding proteins.

In one embodiment of the invention, the DNA adducts, or polynucleotidescomprising the DNA adducts, are removed from the polynucleotides orpolynucleotide pool, such as by a process including heating the solutioncomprising the DNA fragments prior to further processing.

Having thus disclosed exemplary embodiments of the present invention, itshould be noted by those skilled in the art that the disclosures areexemplary only and that various other alternatives, adaptations andmodifications may be made within the scope of the present invention.Accordingly, the present invention is not limited to the specificembodiments as illustrated herein.

Without further elaboration, it is believed that one skilled in the artcan, using the preceding description, utilize the present invention toits fullest extent. The following examples are to be consideredillustrative and thus are not limiting of the remainder of thedisclosure in any way whatsoever.

Example 1 Generation of Random Size Polynucleotides Using U.V. InducedPhotoproducts

One microgram samples of template DNA are obtained and treated with U.V.light to cause the formation of dimers, including TT dimers,particularly purine dimers. U.V. exposure is limited so that only a fewphotoproducts are generated per gene on the template DNA sample.Multiple samples are treated with U.V. light for varying periods of timeto obtain template DNA samples with varying numbers of dimers from U.V.exposure.

A random priming kit which utilizes a non-proofreading polymerase (forexample, Prime-It II Random Primer Labeling kit by Stratagene CloningSystems) is utilized to generate different size polynucleotides bypriming at random sites on templates which are prepared by U.V. light(as described above) and extending along the templates. The primingprotocols such as described in the Prime-It II Random Primer Labelingkit may be utilized to extend the primers. The dimers formed by U.V.exposure serve as a roadblock for the extension by the non-proofreadingpolymerase. Thus, a pool of random size polynucleotides is present afterextension with the random primers is finished.

Example 2 Isolation of Random Size Polynucleotides

Polynucleotides of interest which are generated according to Example 1are gel isolated on a 1.5% agarose gel. Polynucleotides in the 100-300bp range are cut out of the gel and 3 volumes of 6 M NaI is added to thegel slice. The mixture is incubated at 50° C. for 10 minutes and 10 μlof glass milk (Bio 101) is added. The mixture is spun for 1 minute andthe supernatant is decanted. The pellet is washed with 500 μl of ColumnWash (Column Wash is 50% ethanol, 10 mM Tris-HCl pH 7.5, 100 mM NaCl and2.5 mM EDTA) and spin for 1 minute, after which the supernatant isdecanted. The washing, spinning and decanting steps are then repeated.The glass milk pellet is resuspended in 20 μl of H₂O and spun for 1minute. DNA remains in the aqueous phase.

Example 3 Shuffling of Isolated Random Size 100-300 bp Polynucleotides

The 100-300 bp polynucleotides obtained in Example 2 are recombined inan annealing mixture (0.2 mM each dNTP, 2.2 mM MgCl₂, 50 mM KCl, 10 mMTris-HCl ph 8.8, 0.1% Triton X-100, 0.3μ; Taq DNA polymerase, 50 μltotal volume) without adding primers. A Robocycler by Stratagene wasused for the annealing step with the following program: 95° C. for 30seconds, 25-50 cycles of [95° C. for 30 seconds, 50-60° C. (preferably58° C.) for 30 seconds, and 72° C. for 30 seconds] and 5 minutes at 72°C. Thus, the 100-300 bp polynucleotides combine to yield double-strandedpolynucleotides having a longer sequence. After separating out thereassembled double-stranded polynucleotides and denaturing them to formsingle stranded polynucleotides, the cycling is optionally againrepeated with some samples utilizing the single strands as template andprimer DNA and other samples utilizing random primers in addition to thesingle strands.

Example 4

Screening of Polypeptides from Shuffled Polynucleotides

The polynucleotides of Example 3 are separated and polypeptides areexpressed therefrom. The original template DNA is utilized as acomparative control by obtaining comparative polypeptides therefrom. Thepolypeptides obtained from the shuffled polynucleotides of Example 3 arescreened for the activity of the polypeptides obtained from the originaltemplate and compared with the activity levels of the control. Theshuffled polynucleotides coding for interesting polypeptides discoveredduring screening are compared further for secondary desirable traits.Some shuffled polynucleotides corresponding to less interesting screenedpolypeptides are subjected to reshuffling.

Example 5

Directed Evolution an Enzyme by Saturation Mutagenesis

Site-Saturation Mutagenesis: To accomplish site-saturation mutagenesisevery residue (316) of a dehalogenase enzyme was converted into all 20amino acids by site directed mutagenesis using 32-fold degenerateoligonucleotide primers, as follows:

-   1. A culture of the dehalogenase expression construct was grown and    a preparation of the plasmid was made-   2. Primers were made to randomize each codon—they have the common    structure X₂₀NN(G/T)X₂₀-   3. A reaction mix of 25 ul was prepared containing ˜50 ng of plasmid    template, 125 ng of each primer, 1× native Pfu buffer, 200 uM each    DNTP and 2.5 U native Pfu DNA Polymerase-   4. The reaction was cycled in a Robo96 Gradient Cycler as follows:    -   Initial denaturation at 95° C. for 1 min    -   20 cycles of 95° C. for 45 sec, 53° C. for 1 min and 72° C. for        11 min    -   Final elongation step of 72° C. for 10 min-   5. The reaction mix was digested with 10 U of DpnI at 37° C. for 1    hour to digest the methylated template DNA-   6. Two ul of the reaction mix were used to transform 50 ul of    XL1-Blue MRF′ cells and the entire transformation mix was plated on    a large LB-Amp-Met plate yielding 200-1000 colonies-   7. Individual colonies were toothpicked into the wells of 96-well    microtiter plates containing LB-Amp-IPTG and grown overnight-   8. The clones on these plates were assayed the following day    Screening: Approximately 200 clones of mutants for each position    were grown in liquid media (384 well microtiter plates) and screened    as follows:-   1. Overnight cultures in 384-well plates were centrifuged and the    media removed. To each well was added 0.06 mL 1 mM Tris/SO₄ ²⁻ pH    7.8.-   2. Made 2 assay plates from each parent growth plate consisting of    0.02 mL cell suspension.-   3. One assay plate was placed at room temperature and the other at    elevated temperature (initial screen used 55° C.) for a period of    time (initially 30 minutes).-   4. After the prescribed time 0.08 mL room temperature substrate (TCP    saturated 1 mM Tris/SO₄ ²⁻ pH 7.8 with 1.5 mM NaN₃ and 0.1 mM    bromothymol blue) was added to each well.-   5. Measurements at 620 nm were taken at various time points to    generate a progress curve for each well.-   6. Data were analyzed and the kinetics of the cells heated to those    not heated were compared. Each plate contained 1-2 columns (24    wells) of unmutated 20F12 controls.-   7. Wells that appeared to have improved stability were re-grown and    tested under the same conditions.

Following this procedure nine single site mutations appeared to conferincreased thermal stability on the enzyme. Sequence analysis wasperformed to determine of the exact amino acid changes at each positionthat were specifically responsible for the improvement. In sum, theimprovement was conferred at 7 sites by one amino acid change alone, atan eighth site by each of two amino acid changes, and at a ninth site byeach of three amino acid changes. Several mutants were then made eachhaving a plurality of these nine beneficial site mutations incombination; of these two mutants proved superior to all the othermutants, including those with single point mutations.

Example 6 Direct Expression Cloning Using End-Selection

An esterase gene was amplified using 5′phosphorylated primers in astandard PCR reaction (10 ng template; PCR conditions: 3′ 94 C; [1′ 94C; 1′ 50 C; 1′30″ 68 C]×30; 10′ 68 C.

Forward Primer = 9511TopF (CTAGAAGGGAGGAGAATTACATGAAGCGGCTTTTAGCCC)Reverse Primer = 9511TopR (AGCTAAGGGTCAAGGCCGCACCCGAGG)The resulting PCR product (ca. 1000 bp) was gel purified and quantified.

A vector for expression cloning, pASK3 (Institut fuer Bioanalytik,Goettingen, Germany), was cut with Xba I and Bgl II and dephosphorylatedwith CIP.

0.5 pmoles Vaccina Topoisomerase I (Invitrogen, Carlsbad, Calif.) wasadded to 60 ng (ca. 0.1 pmole) purified PCR product for 5′ 37 C inbuffer NEB I (New England Biolabs, Beverly, Mass.) in 5 μl total volume.

The topogated PCR product was cloned into the vector pASK3 (5 μl, ca.200 ng in NEB I) for 5′ at room temperature.

This mixture was dialyzed against H₂O for 30′.

2 μl were used for electroporation of DH10B cells (Gibco BRL,Gaithersburg, Md.).

Efficiency: Based on the actual clone numbers this method can produce2×10⁶ clones per μg vector. All tested recombinants showed esteraseactivity after induction with anhydrotetracycline.

Example 7

Dehalogenase Thermal Stability

This invention provides that a desirable property to be generated bydirected evolution is exemplified in a limiting fashion by an improvedresidual activity (e.g. an enzymatic activity, an immunoreactivity, anantibiotic activity, etc.) of a molecule upon subjection to alteredenvironment, including what may be considered a harsh environment, for aspecified time. Such a harsh environment may comprise any combination ofthe following (iteratively or not, and in any order or permutation): anelevated temperature (including a temperature that may causedenaturation of a working enzyme), a decreased temperature, an elevatedsalinity, a decreased salinity, an elevated pH, a decreased pH, anelevated pressure, a decreassed pressure, and an change in exposure to aradiation source (including uv radiation, visible light, as well as theentire electromagnetic spectrum).

The following example shows an application of directed evolution toevolve the ability of an enzyme to regain &/or retain activity uponexposure to an elevated temperature.

Every residue (316) of a dehalogenase enzyme was converted into all 20amino acids by site directed mutagenesis using 32-fold degenerateoligonucleotide primers. These mutations were introduced into thealready rate-improved variant Dhla 20F12. Approximately 200 clones ofeach position were grown in liquid media (384 well microtiter plates) tobe screened. The screening procedure was as follows:

-   1. Overnight cultures in 384-well plates were centrifuged and the    media removed. To each well was added 0.06 mL 1 mM Tris/SO₄ ²⁻ pH    7.8.-   2. The robot made 2 assay plates from each parent growth plate    consisting of 0.02 mL cell suspension.-   3. One assay plate was placed at room temperature and the other at    elevated temperature (initial screen used 55° C.) for a period of    time (initially 30 minutes).-   4. After the prescribed time 0.08 mL room temperature substrate (TCP    saturated 1 mM Tris/SO₄ ²⁻ pH 7.8 with 1.5 mM NaN₃ and 0.1 mM    bromothymol blue) was added to each well. TCP=trichloropropane.-   5. Measurements at 620 nm were taken at various time points to    generate a progress curve for each well.-   6. Data were analyzed and the kinetics of the cells heated to those    not heated were compared. Each plate contained 1-2 columns (24    wells) of un-mutated 20F12 controls.-   7. Wells that appeared to have improved stability were regrown and    tested under the same conditions.

Following this procedure nine single site mutations appeared to conferincreased thermal stability on Dhla-20F12. Sequence analysis showed thatthe following changes were beneficial:

D89G F91S T159L G189Q, G189V I220L N238T W251Y P302A, P302L, P302S,P302K P302R/S306R

Only two sites (189 and 302) had more than one substitution. The first 5on the list were combined (using G189Q) into a single gene (this mutantis referred to as “Dhlas”). All changes but S306R were incorporated intoanother variant referred to as Dhla8.

Thermal stability was assessed by incubating the enzyme at the elevatedtemperature (55° C. and 80° C.) for some period of time and activityassay at 30° C. Initial rates were plotted vs. time at the highertemperature. The enzyme was in 50 mM Tris/SO₄ pH 7.8 for both theincubation and the assay. Product (Cl⁻) was detected by a standardmethod using Fe(NO₃)₃ and HgSCN. Dhla 20F12 was used as the defacto wildtype. The apparent half-life (T_(1/2)) was calculated by fitting thedata to an exponential decay function.

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1. A method for producing a set of progeny polynucleotides, comprisingthe steps of (a) providing copies of a template polynucleotide, eachcomprising a plurality of codons that encode a template polypeptidesequence; and (b) for each codon of the template polynucleotide,performing the steps of (1) providing a set of degenerate primers,wherein each primer comprises a degenerate codon corresponding to thecodon of the template polynucleotide and at least one adjacent sequencethat is homologous to a sequence adjacent to the codon of the templatepolynucleotide; (2) providing conditions allowing the primers to annealto the copies of the template polynucleotides; and (3) performing apolymerase elongation reaction from the primers along the template;thereby producing progeny polynucleotides, each of which contains asequence corresponding to the degenerate codon of the annealed primer;thereby producing a set of progeny polynucleotides.
 2. The method ofclaim 1, wherein the template polynucleotide is provided indouble-stranded form.
 3. The method of claim 1, wherein the templatepolynucleotide is provided as part of a circular DNA.
 4. The method ofclaim 1, wherein the template polynucleotide is at least 15 bases inlength.
 5. The method of claim 1, wherein the template polynucleotideencodes a polypeptide of at least 100 amino acids.
 6. The method ofclaim 1, wherein the template polynucleotide encodes a whole gene. 7.The method of claim 1, wherein the template polynucleotide encodes anopen reading frame.
 8. The method of claim 1, wherein the primer is asynthetic oligonucleotide.
 9. The method of claim 1, wherein thedegenerate codon is N,N,N.
 10. The method of claim 1, wherein thedegeneracy of the codon is less than 64-fold.
 11. The method of claim10, wherein the degenerate codon is N,N,^(G)/_(T).
 12. The method ofclaim 10, wherein the degenerate codon is N,N,^(G)/_(C).
 13. The methodof claim 10, wherein the degenerate codon is selected from the groupconsisting of N,N,^(C)/G/_(T); N,N,^(A)/G/_(T); and N,N,^(A)/C/_(G). 14.The method of claim 1, wherein the degeneracy of the codon is less than32-fold.
 15. The method of claim 1, wherein the degenerate codon canencode 20 naturally occurring amino acids.
 16. The method of claim 1,wherein the degenerate codon can encode less than 20 naturally occurringamino acids.
 17. The method of claim 16, wherein the degenerate codon isselected from the group comprising N,N,^(G)/_(A); N,N,^(A)/_(C);N,N,^(A)/_(T); N,N,^(C)/_(T); N,N,C; N,N,T; N,N,^(A)/C/_(T);N,^(A)/C/_(G),N; N,^(A)/C/_(T),N; and N,^(A)/G/_(T),N.
 18. The method ofclaim 1, wherein the degenerate codon of the primer is contiguous withthe homologous sequence primer.
 19. The method of claim 1, wherein theprimer comprises a second sequence that is homologous to a secondsequence adjacent to the codon of the template polynucleotide.
 20. Themethod of claim 19, wherein the primer comprises a first homologoussequence, a degenerate codon, and a second homologous sequence.
 21. Themethod of claim 19, wherein a homologous sequence is 20 bases in length.22. The method of claim 21, wherein the first homologous sequence is 20bases in length, the degenerate codon is N,N,G/T, and the secondhomologous sequence is 20 bases in length.
 23. The method of claim 1,wherein the primer comprises a plurality of degenerate codons.
 24. Themethod of claim 23, wherein the primer contains two degenerate codons.25. The method of claim 23, wherein at least two of the plurality ofdegenerate codons are contiguous.
 26. The method of claim 23, wherein atleast two of the plurality of degenerate codons are separated.
 27. Themethod of claim 1, wherein the primer is serviceable for introducing anadditional sequence into the template polynucleotide.
 28. The method ofclaim 1, wherein the primer is serviceable for deleting a sequence fromthe template polynucleotide.
 29. The method of claim 1, wherein a secondprimer is allowed to anneal to the template polynucleotide in step (b)(2).
 30. The method of claim 29, wherein the second primer is a reverseprimer.
 31. The method of claim 29, wherein the second primer is adegenerate primer.
 32. The method of claim 29, wherein the second primeris a nondegenerate primer.
 33. The method of claim 1, wherein step (b)occurs in a single reaction vessel.
 34. The method of claim 33, whereinthe steps of (b) are performed for each codon of the templatepolynucleotide in a separate reaction vessel.
 35. The method of claim33, wherein the steps of (b) are performed for each codon of thetemplate polynucleotide in parallel.
 36. The method of claim 1, whereinthe polymerase is Pfu polymerase.
 37. The method of claim 1, furthercomprising a ligation step.
 38. The method of claim 37, wherein theligation step is performed using T4 DNA ligase.
 39. The method of claim1, further comprising the step of treating the copies of the templatepolynucleotide with a selection enzyme.
 40. The method of claim 39,wherein the template polynucleotide in step (a) is provided inmethylated form; and further comprising the step of (4) digesting thetemplate polynucleotide with DpnI.
 41. The method of claim 1, furthercomprising the step of transforming progeny polynucleotides into a hostcell.
 42. The method of claim 1, further comprising the step ofscreening the progeny polynucleotide for a desired functional property.43. The method of claim 1, further comprising the step of expressing theprogeny polynucleotides to obtain a progeny polypeptide.
 44. The methodof claim 43, further comprising the step of screening the progenypolypeptide for a desired functional property.
 45. The method of claim44, further comprising the step of identifying a progeny polypeptidehaving a desired functional property; and obtaining the polynucleotidesequence encoding the identified polypeptide.